diff --git a/hpg-bigdata-analysis/pom.xml b/hpg-bigdata-analysis/pom.xml
index 768cb6d4..f43f97be 100644
--- a/hpg-bigdata-analysis/pom.xml
+++ b/hpg-bigdata-analysis/pom.xml
@@ -84,6 +84,11 @@
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>
         </dependency>
+        <dependency>
+            <groupId>com.beust</groupId>
+            <artifactId>jcommander</artifactId>
+            <version>1.58</version>
+        </dependency>
     </dependencies>
 
 </project>
\ No newline at end of file
diff --git a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/AnalysisExecutor.java b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/AnalysisExecutor.java
index 9444df34..8ec3aafd 100644
--- a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/AnalysisExecutor.java
+++ b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/AnalysisExecutor.java
@@ -4,15 +4,19 @@
  * Created by jtarraga on 30/01/17.
  */
 public abstract class AnalysisExecutor {
-    protected String datasetName;
+    protected String studyId;
 
-    public String getDatasetName() {
-        return datasetName;
+    protected AnalysisExecutor(String studyId) {
+        this.studyId = studyId;
     }
 
-    public void setDatasetName(String datasetName) {
-        this.datasetName = datasetName;
+    protected String studyId() {
+        return studyId;
     }
 
-    public abstract void execute() throws AnalysisExecutorException;
+    protected void setStudyId(String studyId) {
+        this.studyId = studyId;
+    }
+
+    protected abstract void execute() throws AnalysisExecutorException;
 }
diff --git a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/FilterParameters.java b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/FilterParameters.java
new file mode 100644
index 00000000..bdbb7e66
--- /dev/null
+++ b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/FilterParameters.java
@@ -0,0 +1,105 @@
+package org.opencb.hpg.bigdata.analysis.variant;
+
+import com.beust.jcommander.Parameter;
+
+public class FilterParameters {
+    @Parameter(names = {"--id"}, description = "Query for ID; comma separated list of IDs, e.g.:"
+            + " \"rs312411,rs421225\"", arity = 1)
+    public String ids;
+
+    @Parameter(names = {"--id-file"}, description = "Query for ID that are stored in a file, one ID per line,"
+            + " e.g.: rs312411", arity = 1)
+    public String idFilename;
+
+    @Parameter(names = {"--type"}, description = "Query for type; comma separated list of IDs, e.g.:"
+            + " \"INDEL,SNP,SNV\"", arity = 1)
+    public String types;
+
+    @Parameter(names = {"--s", "--study"}, description = "Query for study; comma separated list of study names",
+            arity = 1)
+    public String studies;
+
+    @Parameter(names = {"--biotype"}, description = "Query for biotype; comma separated list of biotype names,"
+            + " e.g.: protein_coding, pseudogene", arity = 1)
+    public String biotypes;
+
+    @Parameter(names = {"-r", "--region"}, description = "Query for region; comma separated list of regions,"
+            + " e.g.: 1:300000-400000000,15:343453463-8787665654", arity = 1)
+    public String regions;
+
+    @Parameter(names = {"--region-file"}, description = "Query for regions that are stored in a file, one region"
+            + " per line,  e.g.: 1:6700000-560000000", arity = 1)
+    public String regionFilename;
+
+    @Parameter(names = {"--maf"}, description = "Query for the Minor Allele Frequency of a given study and"
+            + " cohort. Use the following format enclosed with double quotes: \"study_name::cohort_name"
+            + "[<|>|<=|>=|==|!=]value\", e.g.: \"1000g::all>0.4\"", arity = 1)
+    public String maf;
+
+    @Parameter(names = {"--mgf"}, description = "Query for the Minor Genotype Frequency of a given study and"
+            + " cohort. Use the following format enclosed with double quotes: \"study_name::cohort_name"
+            + "[<|>|<=|>=|==|!=]value\", e.g.: \"1000g::all>0.18198\"", arity = 1)
+    public String mgf;
+
+    @Parameter(names = {"--missing-allele"}, description = "Query for the number of missing alleles of a given"
+            + " study and cohort. Use the following format enclosed with double quotes: \"study_name::cohort_name"
+            + "[<|>|<=|>=|==|!=]value\", e.g.: \"1000g::all==5\"", arity = 1)
+    public String missingAlleles;
+
+    @Parameter(names = {"--missing-genotype"}, description = "Query for the number of missing genotypes of a"
+            + " given study and cohort. Use the following format enclosed with double quotes: \"study_name::"
+            + "cohort_name[<|>|<=|>=|==|!=]value\", e.g.: \"1000g::all!=0\"", arity = 1)
+    public String missingGenotypes;
+
+    @Parameter(names = {"--ct", "--consequence-type"}, description = "Query for Sequence Ontology term names or"
+            + " accession codes; comma separated (use double quotes if you provide term names), e.g.:"
+            + " \"transgenic insertion,SO:32234,SO:00124\"", arity = 1)
+    public String consequenceTypes;
+
+    @Parameter(names = {"--gene"}, description = "Query for gene; comma separated list of gene names, e.g.:"
+            + " \"BIN3,ZNF517\"", arity = 1)
+    public String genes;
+
+    @Parameter(names = {"--clinvar"}, description = "Query for clinvar (accession); comma separated list of"
+            + " accessions", arity = 1)
+    public String clinvar;
+
+    @Parameter(names = {"--cosmic"}, description = "Query for cosmic (mutation ID); comma separated list of"
+            + " mutations IDs", arity = 1)
+    public String cosmic;
+
+//        @Parameter(names = {"--gwas"}, description = "Query for gwas (traits); comma separated list of traits",
+// arity = 1)
+//        public String gwas;
+
+    @Parameter(names = {"--conservation"}, description = "Query for conservation scores (phastCons, phylop, gerp);"
+            + "comma separated list of scores and enclosed with double quotes, e.g.: \"phylop<0.3,phastCons<0.1\"",
+            arity = 1)
+    public String conservScores;
+
+    @Parameter(names = {"--ps", "--protein-substitution"}, description = "Query for protein substitution scores"
+            + " (polyphen, sift); comma separated list of scores and enclosed with double quotes, e.g.:"
+            + "\"polyphen>0.3,sift>0.6\"", arity = 1)
+    public String substScores;
+
+    @Parameter(names = {"--pf", "--population-frequency"}, description = "Query for alternate population"
+            + " frequency of a given study. Use the following format enclosed with double quotes:"
+            + " \"study_name::population_name[<|>|<=|>=|==|!=]frequency_value\", e.g.: \"1000g::CEU<0.4\"",
+            arity = 1)
+    public String pf;
+
+    @Parameter(names = {"--pmaf", "--population-maf"}, description = "Query for population minor allele frequency"
+            + " of a given study. Use the following the format enclosed with double quotes: \"study_name::"
+            + "population_name[<|>|<=|>=|==|!=]frequency_value\", e.g.: \"1000g::PJL<=0.25\"", arity = 1)
+    public String pmaf;
+
+    @Parameter(names = {"--sample-genotype"}, description = "Query for sample genotypes. Use the following the"
+            + " format enclosed with double quotes: \"sample_name1:genotype1,genotype;sample_name2:genotype1\","
+            + " e.g.: \"HG00112:0/0;HG23412:1/0,1/1\"", arity = 1)
+    public String sampleGenotypes;
+
+    @Parameter(names = {"--sample-filter"}, description = "Query for sample filter, i.e.: individual attributes (family, father,"
+            + " mother, sex and phenotype) and user-defined attributes from pedigree information,"
+            + "  e.g.: \"individual.sex=MALE;Eyes=Blue\"", arity = 1)
+    public String sampleFilters;
+}
diff --git a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/LinearRegressionAnalysis.java b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/LinearRegressionAnalysis.java
index b83b5f89..ca5ca534 100644
--- a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/LinearRegressionAnalysis.java
+++ b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/LinearRegressionAnalysis.java
@@ -63,14 +63,13 @@ public void execute() {
         System.out.println("r2: " + trainingSummary.r2());
     }
 
-    public LinearRegressionAnalysis(String datasetName, String studyName, String depVarName, String indepVarName) {
-        this(datasetName, studyName, depVarName, indepVarName, 10, 0.3, 0.8);
+    public LinearRegressionAnalysis(String studyId, String depVarName, String indepVarName) {
+        this(studyId, depVarName, indepVarName, 10, 0.3, 0.8);
     }
 
-    public LinearRegressionAnalysis(String datasetName, String studyName, String depVarName, String indepVarName,
+    public LinearRegressionAnalysis(String studyId, String depVarName, String indepVarName,
                                     int numIterations, double regularization, double elasticNet) {
-        this.datasetName = datasetName;
-        this.studyName = studyName;
+        super(studyId);
         this.depVarName = depVarName;
         this.indepVarName = indepVarName;
         this.numIterations = numIterations;
diff --git a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/LogisticRegressionAnalysis.java b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/LogisticRegressionAnalysis.java
index 4b58c3e3..d02a20e7 100644
--- a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/LogisticRegressionAnalysis.java
+++ b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/LogisticRegressionAnalysis.java
@@ -70,14 +70,13 @@ public void execute() {
         lrModel.setThreshold(bestThreshold);
     }
 
-    public LogisticRegressionAnalysis(String datasetName, String studyName, String depVarName, String indepVarName) {
-        this(datasetName, studyName, depVarName, indepVarName, 10, 0.3, 0.8);
+    public LogisticRegressionAnalysis(String studyId, String depVarName, String indepVarName) {
+        this(studyId, depVarName, indepVarName, 10, 0.3, 0.8);
     }
 
-    public LogisticRegressionAnalysis(String datasetName, String studyName, String depVarName, String indepVarName,
+    public LogisticRegressionAnalysis(String studyId, String depVarName, String indepVarName,
                                       int numIterations, double regularization, double elasticNet) {
-        this.datasetName = datasetName;
-        this.studyName = studyName;
+        super(studyId);
         this.depVarName = depVarName;
         this.indepVarName = indepVarName;
         this.numIterations = numIterations;
diff --git a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/PCAAnalysis.java b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/PCAAnalysis.java
index 52deb02e..af33e6c9 100644
--- a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/PCAAnalysis.java
+++ b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/PCAAnalysis.java
@@ -29,13 +29,12 @@ public void execute() {
         result.show(false);
     }
 
-    public PCAAnalysis(String datasetName, String studyName, String featureName) {
-        this(datasetName, studyName, featureName, 3);
+    public PCAAnalysis(String studyId, String studyName, String featureName) {
+        this(studyId, studyName, featureName, 3);
     }
 
-    public PCAAnalysis(String datasetName, String studyName, String featureName, int kValue) {
-        this.datasetName = datasetName;
-        this.studyName = studyName;
+    public PCAAnalysis(String studyId, String studyName, String featureName, int kValue) {
+        super(studyId);
         this.featureName = featureName;
         this.kValue = kValue;
     }
diff --git a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/RvTestsAdaptor.java b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/RvTestsAdaptor.java
deleted file mode 100644
index df9d9f07..00000000
--- a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/RvTestsAdaptor.java
+++ /dev/null
@@ -1,468 +0,0 @@
-package org.opencb.hpg.bigdata.analysis.variant;
-
-import org.apache.spark.SparkConf;
-import org.apache.spark.SparkContext;
-import org.apache.spark.api.java.JavaPairRDD;
-import org.apache.spark.api.java.JavaRDD;
-import org.apache.spark.api.java.function.Function;
-import org.apache.spark.sql.Dataset;
-import org.apache.spark.sql.Row;
-import org.apache.spark.sql.SparkSession;
-import org.opencb.biodata.formats.pedigree.PedigreeManager;
-import org.opencb.biodata.models.core.Region;
-import org.opencb.biodata.models.core.pedigree.Pedigree;
-import org.opencb.biodata.tools.variant.metadata.VariantMetadataManager;
-import org.opencb.commons.utils.FileUtils;
-import org.opencb.hpg.bigdata.analysis.AnalysisExecutor;
-import org.opencb.hpg.bigdata.analysis.AnalysisExecutorException;
-import org.opencb.hpg.bigdata.core.lib.SparkConfCreator;
-import org.opencb.hpg.bigdata.core.lib.VariantDataset;
-import scala.Tuple2;
-import scala.collection.mutable.StringBuilder;
-import scala.collection.mutable.WrappedArray;
-
-import java.io.*;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.*;
-
-/**
- * Created by joaquin on 1/19/17.
- */
-public class RvTestsAdaptor extends AnalysisExecutor implements Serializable {
-    private String inFilename;
-    private String metaFilename;
-    private String outDirname;
-    private String confFilename;
-
-    private final String RVTEST_BIN = "rvtests"; //"/home/jtarraga/soft/rvtests/executable/rvtest";
-    private final String BGZIP_BIN = "bgzip"; //"/home/joaquin/softs/htslib/bgzip";
-    private final String TABIX_BIN = "tabix"; //"/home/joaquin/softs/htslib/tabix";
-
-    public RvTestsAdaptor(String inFilename, String outDirname, String confFilename) {
-        this(inFilename, inFilename + ".meta.json", outDirname, confFilename);
-    }
-
-    public RvTestsAdaptor(String inFilename, String metaFilename, String outDirname, String confFilename) {
-        this.inFilename = inFilename;
-        this.metaFilename = metaFilename;
-        this.outDirname = outDirname;
-        this.confFilename = confFilename;
-    }
-
-//    ./build/bin/hpg-bigdata-local2.sh variant rvtests -i ~/data/vcf/skat/example.vcf.avro -o ~/data/vcf/skat/out
-// --dataset noname -c ~/data/vcf/skat/skat.params
-
-    public void run(String datasetName) throws Exception {
-        // create spark session
-        SparkConf sparkConf;
-        if (inFilename.startsWith("/")) {
-            sparkConf = SparkConfCreator.getConf("variant rvtests", "local", 1, true);
-        } else {
-            sparkConf = new SparkConf().setAppName("variant rvtests");
-        }
-        SparkSession sparkSession = new SparkSession(new SparkContext(sparkConf));
-
-        // load dataset
-        VariantDataset vd = new VariantDataset(sparkSession);
-        vd.load(inFilename);
-        vd.createOrReplaceTempView("vcf");
-
-        // load rvtests parameters into properties
-        Properties props = new Properties();
-        InputStream confStream = new FileInputStream(confFilename);
-        props.load(confStream);
-        confStream.close();
-
-        for (Object key: props.keySet()) {
-            System.out.println((String) key + " = " + (String) props.get(key));
-        }
-
-        List<String> kernels = null;
-        String kernel = props.getProperty("kernel");
-        if (kernel != null) {
-            kernels = Arrays.asList(kernel.toLowerCase()
-                    .replace("skato", "SkatO")
-                    .replace("skat", "Skat")
-                    .split(","));
-        }
-
-        // create temporary directory
-        File tmpDir = new File(outDirname + "/tmp");
-        tmpDir.mkdir();
-
-        // create temporary file for --pheno
-        File phenoFile = new File(tmpDir.getAbsolutePath() + "/pheno");
-        VariantMetadataManager metadataManager = new VariantMetadataManager();
-        metadataManager.load(Paths.get(metaFilename));
-        Pedigree pedigree = metadataManager.getPedigree(datasetName);
-        new PedigreeManager().save(pedigree, phenoFile.toPath());
-
-        // loop for regions
-        String line;
-        BufferedWriter writer =  null;
-        BufferedReader reader = FileUtils.newBufferedReader(Paths.get(props.getProperty("setFile")));
-        int i = 0;
-        StringBuilder sb = new StringBuilder();
-        while ((line = reader.readLine()) != null) {
-            String[] fields = line.split("[\t ]");
-            System.out.println(fields[0]);
-            Region region = new Region(fields[1]);
-
-            // create temporary files for --inVcf and --setFile
-            File setFile = new File(tmpDir.getAbsolutePath() + "/setFile." + i);
-            writer = FileUtils.newBufferedWriter(setFile.toPath());
-            writer.write(fields[0] + "\t" + fields[1] + "\n");
-            writer.close();
-
-            // create temporary vcf file fot the region variants
-            VariantDataset ds = (VariantDataset) vd.regionFilter(region);
-            File vcfFile = new File(tmpDir.getAbsolutePath() + "/variants." + i + ".vcf");
-            writer = FileUtils.newBufferedWriter(vcfFile.toPath());
-
-            // header lines
-            writer.write("##fileformat=VCFv4.2\n");
-            writer.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
-            // sample names
-            for (String key: pedigree.getIndividuals().keySet()) {
-                writer.write("\t");
-                writer.write(pedigree.getIndividuals().get(key).getId());
-            }
-            writer.write("\n");
-
-            // variant lines
-//            writer.write(i + " >>>>>>>>>>>>>> " + line + ", num. rows = " + ds.count() + "\n");
-//            writer.close();
-//            System.out.println("\n\n" + i + " >>>>>>>>>>>>>> " + line + ", num. rows = " + ds.count() + "\n");
-//            ds.show(1, false);
-//            ds.reset();
-
-            //System.out.println("----------> !!!! rows should be sorted by start !!!" + ds.getSql());
-//            ds.executeSql(ds.getSql()).show();
-//            System.out.println("----------> rows should be sorted by start !!!");
-//            ds.executeSql("SELECT * FROM vcf  WHERE (chromosome = '22' AND start >= 32755892 AND end <= 32767063)"
-//                    + " ORDER BY start ASC").show();
-//            System.exit(0);
-
-            //List<Row> rows = ds.collectAsList();
-            List<Row> rows = ds.executeSql(ds.getSql()).collectAsList();
-            ds.reset();
-
-            for (Row row: rows) {
-                List<Row> studies = row.getList(12);
-                Row study = null;
-                for (int j = 0; j < studies.size(); j++) {
-                    if (studies.get(j).get(0).equals(datasetName)) {
-                        study = studies.get(j);
-                        break;
-                    }
-                }
-
-                if (study == null) {
-                    throw new Exception("Dataset '" + datasetName + "' not found!");
-                }
-
-//              System.out.println("\n\n\n" + row.mkString() + "\n\n");
-                List<Row> files = study.getList(1);
-                String filter = (String) files.get(0).getJavaMap(2).get("FILTER");
-                String qual = (String) files.get(0).getJavaMap(2).get("QUAL");
-
-                sb.setLength(0);
-                sb.append(row.get(2)).append("\t").append(row.get(3)).append("\t")
-                        .append(row.get(0) == null ? "." : row.get(0)).append("\t")
-                        .append(row.get(5)).append("\t").append(row.get(6)).append("\t").append(qual).append("\t")
-                        .append(filter).append("\t").append(".").append("\t").append(study.getList(3).get(0));
-
-                int j = 0;
-                try {
-//                    System.out.println("size for (" + i + "): " + sb.toString());
-//                    System.out.println("\tsize = " + study.getList(4).size());
-                    for (j = 0; j < pedigree.getIndividuals().size(); j++) {
-//                        System.out.println(j + ": ");
-//                        System.out.println("\t" + ((WrappedArray) study.getList(4).get(j)).head());
-                        sb.append("\t").append(((WrappedArray) study.getList(4).get(j)).head());
-                    }
-                } catch (Exception ex) {
-                    System.out.println("Exception for sample data: " + sb.toString());
-                    System.out.println("(i, j, sample data size, pedigree size)  = ("
-                            + i + ", " + j + ", " + study.getList(4).size() + ", " + pedigree.getIndividuals().size());
-                    System.out.println(ex.getMessage());
-                    ex.printStackTrace();
-                }
-                sb.append("\n");
-                writer.write(sb.toString());
-//                System.out.println(sb.toString());
-            }
-            writer.close();
-
-            // compress vcf to bgz
-            sb.setLength(0);
-            sb.append(props.getProperty("bgzip", this.BGZIP_BIN)).append(" ").append(vcfFile.getAbsolutePath());
-            execute(sb.toString(), "Compressing vcf to gz: " + sb.toString());
-
-            // and create tabix index
-            sb.setLength(0);
-            sb.append(props.getProperty("tabix", this.TABIX_BIN)).append(" -p vcf ").append(vcfFile.getAbsolutePath()).append(".gz");
-            execute(sb.toString(), "Creating tabix index: " + sb);
-
-            // rvtests command line
-            sb.setLength(0);
-            sb.append(props.getProperty("rvtests", this.RVTEST_BIN))
-                    .append(kernel == null ? " " : " --kernel " + kernel)
-                    .append(" --pheno ").append(phenoFile.getAbsolutePath())
-                    .append(" --inVcf ").append(vcfFile.getAbsolutePath()).append(".gz")
-                    .append(" --setFile ").append(setFile.getAbsolutePath())
-                    .append(" --out ").append(tmpDir.getAbsolutePath()).append("/out.").append(i);
-            execute(sb.toString(), "Running rvtests: " + sb);
-
-            i++;
-        }
-
-        // write final
-        for (String k: kernels) {
-            boolean header = false;
-            writer = FileUtils.newBufferedWriter(Paths.get(outDirname + "/out." + k + ".assoc"));
-            for (int j = 0; j < i; j++) {
-                File file = new File(tmpDir.getAbsolutePath() + "/out." + j + "." + k + ".assoc");
-                if (file.exists()) {
-                    reader = FileUtils.newBufferedReader(file.toPath());
-                    line = reader.readLine();
-                    if (!header) {
-                        writer.write(line);
-                        writer.write("\n");
-                        header = true;
-                    }
-                    while ((line = reader.readLine()) != null) {
-                        writer.write(line);
-                        writer.write("\n");
-                    }
-                    reader.close();
-                }
-            }
-            writer.close();
-        }
-    }
-
-    public void run00(String datasetName) throws Exception {
-        // create spark session
-        SparkConf sparkConf;
-        if (inFilename.startsWith("/")) {
-            sparkConf = SparkConfCreator.getConf("variant rvtests", "local", 1, true);
-        } else {
-            sparkConf = new SparkConf().setAppName("variant rvtests");
-        }
-        SparkSession sparkSession = new SparkSession(new SparkContext(sparkConf));
-
-        // load dataset
-        VariantDataset vd = new VariantDataset(sparkSession);
-        vd.load(inFilename);
-        vd.createOrReplaceTempView("vcf");
-
-        // load rvtests parameters into properties
-        Properties props = new Properties();
-        InputStream confStream = new FileInputStream(confFilename);
-        props.load(confStream);
-        confStream.close();
-
-        List<String> kernels = null;
-        String kernel = props.getProperty("kernel");
-        if (kernel != null) {
-            kernels = Arrays.asList(kernel.toLowerCase()
-                    .replace("skato", "SkatO")
-                    .replace("skat", "Skat")
-                    .split(","));
-        }
-
-        // create temporary directory
-        File tmpDir = new File(outDirname + "/tmp");
-        tmpDir.mkdir();
-
-        // create temporary file for --pheno
-        File phenoFile = new File(tmpDir.getAbsolutePath() + "/pheno");
-        VariantMetadataManager metadataManager = new VariantMetadataManager();
-        metadataManager.load(Paths.get(metaFilename));
-        Pedigree pedigree = metadataManager.getPedigree(datasetName);
-        new PedigreeManager().save(pedigree, phenoFile.toPath());
-
-        Map<String, String> pedigreeMap = new LinkedHashMap<>();
-        for (String key : pedigree.getIndividuals().keySet()) {
-            pedigreeMap.put(key, pedigree.getIndividuals().get(key).getId());
-        }
-
-        String sql = "SELECT * FROM vcf";
-        Dataset<Row> rows = vd.sqlContext().sql(sql);
-
-        List<String> regions = new ArrayList<>();
-        regions.add("22:40766594-40806293");
-        regions.add("22:32755892-32767063");
-        regions.add("22:32755894-32766972");
-        regions.add("22:29834571-29838444");
-        regions.add("22:31835344-31885547");
-        regions.add("22:31608249-31676066");
-        regions.add("22:38615297-38668670");
-        regions.add("22:38822332-38851203");
-        regions.add("22:20455993-20461786");
-
-        JavaPairRDD<String, Iterable<Row>> groups = rows.javaRDD().groupBy(row -> {
-            String key = null;
-            for (String region: regions) {
-                String[] fields = region.split("[:-]");
-                if (fields[0].equals(row.getString(2))
-                        && Integer.parseInt(fields[1]) <= row.getInt(4)
-                        && Integer.parseInt(fields[2]) >= row.getInt(3)) {
-                    key = region;
-                    break;
-                }
-            }
-            return key;
-        });
-
-        JavaRDD<String> results = groups.map(new Function<Tuple2<String, Iterable<Row>>, String>() {
-            @Override
-            public String call(Tuple2<String, Iterable<Row>> tuple) throws Exception {
-                StringBuilder sb = new StringBuilder();
-                BufferedWriter writer;
-                Iterator<Row> iterator = tuple._2.iterator();
-//                System.out.println("+++++++++++++ " + tuple._1);
-
-                String id = tuple._1.replace(":", "_").replace("-", "_");
-
-                // create temporary files for --inVcf and --setFile
-                File setFile = new File(tmpDir.getAbsolutePath() + "/setFile." + id);
-                writer = FileUtils.newBufferedWriter(setFile.toPath());
-                writer.write(id + "\t" + tuple._1 + "\n");
-                writer.close();
-
-                File vcfFile = new File(tmpDir.getAbsolutePath() + "/variants."
-                        +  id + ".vcf");
-                writer = FileUtils.newBufferedWriter(vcfFile.toPath());
-                // header lines
-                writer.write("##fileformat=VCFv4.2\n");
-                writer.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
-                // sample names
-                for (String key : pedigreeMap.keySet()) {
-                    writer.write("\t");
-                    writer.write(pedigreeMap.get(key));
-                }
-                writer.write("\n");
-                while (iterator.hasNext()) {
-                    Row row = iterator.next();
-//                    System.out.println("=================== " + row);
-
-                    // variant lines
-                    List<Row> studies = row.getList(12);
-                    Row study = null;
-                    for (int j = 0; j < studies.size(); j++) {
-                        if (studies.get(j).get(0).equals(datasetName)) {
-                            study = studies.get(j);
-                            break;
-                        }
-                    }
-
-                    if (study == null) {
-                        throw new Exception("Dataset '" + datasetName + "' not found!");
-                    }
-                    List<Row> files = study.getList(1);
-                    String filter = (String) files.get(0).getJavaMap(2).get("FILTER");
-                    String qual = (String) files.get(0).getJavaMap(2).get("QUAL");
-
-                    sb.setLength(0);
-                    sb.append(row.get(2)).append("\t").append(row.get(3)).append("\t")
-                            .append(row.get(0) == null ? "." : row.get(0)).append("\t")
-                            .append(row.get(5)).append("\t").append(row.get(6)).append("\t").append(qual).append("\t")
-                            .append(filter).append("\t").append(".").append("\t").append(study.getList(3).get(0));
-
-                    for (int j = 0; j < pedigreeMap.size(); j++) {
-                        sb.append("\t").append(((WrappedArray) study.getList(4).get(j)).head());
-                    }
-                    sb.append("\n");
-                    writer.write(sb.toString());
-                    System.out.println(sb.toString());
-                }
-                writer.close();
-
-                // compress vcf to bgz
-                sb.setLength(0);
-                sb.append(props.getProperty("bgzip")).append(" ").append(vcfFile.getAbsolutePath());
-                execute(sb.toString(), "Compressing vcf to gz: " + sb);
-
-                // and create tabix index
-                sb.setLength(0);
-                sb.append(props.getProperty("tabix")).append(" -p vcf ").append(vcfFile.getAbsolutePath()).append(".gz");
-                execute(sb.toString(), "Creating tabix index: " + sb);
-
-                // rvtests command line
-                sb.setLength(0);
-                sb.append(props.getProperty("rvtests"))
-                        .append(kernel == null ? " " : " --kernel " + kernel)
-                        .append(" --pheno ").append(phenoFile.getAbsolutePath())
-                        .append(" --inVcf ").append(vcfFile.getAbsolutePath()).append(".gz")
-                        .append(" --setFile ").append(setFile.getAbsolutePath())
-                        .append(" --out ").append(tmpDir.getAbsolutePath()).append("/out.").append(id);
-                execute(sb.toString(), "Running rvtests: " + sb);
-
-                sb.setLength(0);
-                File file = new File(tmpDir.getAbsolutePath() + "/out." + id + ".Skat.assoc");
-                if (file.exists()) {
-                    BufferedReader reader = FileUtils.newBufferedReader(file.toPath());
-                    String line = reader.readLine();
-                    while ((line = reader.readLine()) != null) {
-                        sb.append(line).append("\n");
-                    }
-                    reader.close();
-                }
-
-                return sb.toString();
-            }
-        });
-
-        System.out.println(results.collect());
-    }
-
-    private Process execute(String cmdline, String label) {
-        Process p = null;
-        try {
-            System.out.println(label);
-            System.out.println("Executing: " + cmdline);
-            p = Runtime.getRuntime().exec(cmdline);
-
-            System.out.println("\tSTDOUT:");
-            System.out.println(readInputStream(p.getInputStream()));
-            System.out.println("\tSTDERR:");
-            System.out.println(readInputStream(p.getErrorStream()));
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
-        return p;
-    }
-
-    private void saveStream(InputStream inputStream, Path path) {
-        try {
-            PrintWriter writer = new PrintWriter(path.toFile());
-            writer.write(readInputStream(inputStream));
-            writer.close();
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
-    }
-
-    private String readInputStream(InputStream inputStream) {
-        StringBuilder res = new StringBuilder();
-        try {
-            // read the output from the command
-            BufferedReader stdInput = new BufferedReader(new InputStreamReader(inputStream));
-            String s;
-            System.out.println("Here is the standard output of the command:\n");
-            while ((s = stdInput.readLine()) != null) {
-                res.append(s).append("\n");
-            }
-        } catch (IOException e) {
-            res.append(e.getMessage()).append("\n");
-        }
-        return res.toString();
-    }
-
-    @Override
-    public void execute() throws AnalysisExecutorException {
-    }
-}
diff --git a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/VariantAnalysisExecutor.java b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/VariantAnalysisExecutor.java
index 6e3fa4e0..ad9f8891 100644
--- a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/VariantAnalysisExecutor.java
+++ b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/VariantAnalysisExecutor.java
@@ -7,13 +7,7 @@
  */
 public abstract class VariantAnalysisExecutor extends AnalysisExecutor {
 
-    protected String studyName;
-
-    public String getStudyName() {
-        return studyName;
-    }
-
-    public void setStudyName(String studyName) {
-        this.studyName = studyName;
+    protected VariantAnalysisExecutor(String studyId) {
+        super(studyId);
     }
 }
diff --git a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/VariantAnalysisUtils.java b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/VariantAnalysisUtils.java
new file mode 100644
index 00000000..e110b568
--- /dev/null
+++ b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/VariantAnalysisUtils.java
@@ -0,0 +1,287 @@
+package org.opencb.hpg.bigdata.analysis.variant;
+
+import htsjdk.variant.variantcontext.writer.Options;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.SparkContext;
+import org.apache.spark.sql.SparkSession;
+import org.opencb.biodata.formats.pedigree.PedigreeManager;
+import org.opencb.biodata.models.core.Region;
+import org.opencb.biodata.models.core.pedigree.Pedigree;
+import org.opencb.biodata.models.metadata.Sample;
+import org.opencb.biodata.models.variant.metadata.VariantStudyMetadata;
+import org.opencb.biodata.tools.variant.converters.VCFExporter;
+import org.opencb.biodata.tools.variant.metadata.VariantMetadataManager;
+import org.opencb.commons.datastore.core.Query;
+import org.opencb.hpg.bigdata.core.lib.SparkConfCreator;
+import org.opencb.hpg.bigdata.core.lib.VariantDataset;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import static java.nio.file.Paths.get;
+
+public class VariantAnalysisUtils {
+    public static final Pattern OPERATION_PATTERN = Pattern.compile("([^=<>~!]+)(.*)$");
+
+    public static void exportVCF(String inputAvroFilename, String metaFilename,
+                                 FilterParameters filterParams, String vcfFilename) {
+        // Generate VCF file by calling VCF exporter from query and query options
+        VariantMetadataManager manager = new VariantMetadataManager();
+        try {
+            manager.load(Paths.get(metaFilename));
+
+            SparkConf sparkConf = SparkConfCreator.getConf("tool plink", "local", 1, true);
+            SparkSession sparkSession = new SparkSession(new SparkContext(sparkConf));
+
+            VariantDataset vd = new VariantDataset(sparkSession);
+            vd.load(inputAvroFilename);
+            vd.createOrReplaceTempView("vcf");
+
+            // Add filters to variant dataset
+            if (filterParams != null) {
+                addVariantFilters(filterParams, vd);
+            }
+
+            // out filename
+            VariantStudyMetadata studyMetadata = manager.getVariantMetadata().getStudies().get(0);
+            VCFExporter vcfExporter = new VCFExporter(studyMetadata);
+            vcfExporter.open(Options.ALLOW_MISSING_FIELDS_IN_HEADER, Paths.get(vcfFilename));
+
+            vcfExporter.export(vd.iterator());
+
+            // close everything
+            vcfExporter.close();
+            sparkSession.stop();
+        } catch (Exception e) {
+            System.out.println("Error retrieving variants from Avro to VCF file: " + e.getMessage());
+        }
+    }
+
+    public static void addVariantFilters(FilterParameters filterParams, VariantDataset vd) throws IOException {
+        VariantMetadataManager metadataManager = new VariantMetadataManager();
+        //metadataManager.load(Paths.get(variantCommandOptions.queryVariantCommandOptions.input + ".meta.json"));
+
+        // query for ID (list and file)
+        List<String> list = null;
+        if (StringUtils.isNotEmpty(filterParams.ids)) {
+            list = Arrays.asList(StringUtils.split(filterParams.ids, ","));
+        }
+        String idFilename = filterParams.idFilename;
+        if (StringUtils.isNotEmpty(idFilename) && new File(idFilename).exists()) {
+            if (list == null) {
+                list = Files.readAllLines(get(idFilename));
+            } else {
+                list.addAll(Files.readAllLines(get(idFilename)));
+            }
+        }
+        if (list != null) {
+            vd.idFilter(list, false);
+        }
+
+        // query for type
+        if (StringUtils.isNotEmpty(filterParams.types)) {
+            vd.typeFilter(Arrays.asList(
+                    StringUtils.split(filterParams.types, ",")));
+        }
+
+        // query for biotype
+        if (StringUtils.isNotEmpty(filterParams.biotypes)) {
+            vd.annotationFilter("biotype", Arrays.asList(
+                    StringUtils.split(filterParams.biotypes, ",")));
+        }
+
+        // query for study
+        if (StringUtils.isNotEmpty(filterParams.studies)) {
+            vd.studyFilter("studyId", Arrays.asList(
+                    StringUtils.split(filterParams.studies, ",")));
+        }
+
+        // query for maf (study:cohort)
+        if (StringUtils.isNotEmpty(filterParams.maf)) {
+            vd.studyFilter("stats.maf", filterParams.maf);
+        }
+
+        // query for mgf (study:cohort)
+        if (StringUtils.isNotEmpty(filterParams.mgf)) {
+            vd.studyFilter("stats.mgf", filterParams.mgf);
+        }
+
+        // query for number of missing alleles (study:cohort)
+        if (StringUtils.isNotEmpty(filterParams.missingAlleles)) {
+            vd.studyFilter("stats.missingAlleles", filterParams.missingAlleles);
+        }
+
+        // query for number of missing genotypes (study:cohort)
+        if (StringUtils.isNotEmpty(filterParams.missingGenotypes)) {
+            vd.studyFilter("stats.missingGenotypes", filterParams.missingGenotypes);
+        }
+
+        // query for region (list and file)
+        List<Region> regions = getRegionList(filterParams.regions,
+                filterParams.regionFilename);
+        if (regions != null && regions.size() > 0) {
+            vd.regionFilter(regions);
+        }
+
+        // query for sample genotypes and/or sample filters
+        StringBuilder sampleGenotypes = new StringBuilder();
+        if (StringUtils.isNotEmpty(filterParams.sampleGenotypes)) {
+            sampleGenotypes.append(filterParams.sampleGenotypes);
+        }
+        String sampleFilters = filterParams.sampleFilters;
+        if (StringUtils.isNotEmpty(sampleGenotypes) || StringUtils.isNotEmpty(sampleFilters)) {
+            // TODO: we need the ID for dataset target
+            List<Sample> samples = null;
+
+
+            if (StringUtils.isNotEmpty(sampleFilters)) {
+                Query sampleQuery = new Query();
+//                final Pattern OPERATION_PATTERN = Pattern.compile("([^=<>~!]+.*)(<=?|>=?|!=|!?=?~|==?)([^=<>~!]+.*)$");
+                String[] splits = sampleFilters.split("[;]");
+                for (int i = 0; i < splits.length; i++) {
+                    Matcher matcher = OPERATION_PATTERN.matcher(splits[i]);
+                    if (matcher.matches()) {
+                        sampleQuery.put(matcher.group(1), matcher.group(2));
+                    }
+                }
+
+                samples = metadataManager.getSamples(sampleQuery,
+                        metadataManager.getVariantMetadata().getStudies().get(0).getId());
+
+                for (Sample sample : samples) {
+                    if (sampleGenotypes.length() > 0) {
+                        sampleGenotypes.append(";");
+                    }
+                    //sampleGenotypes.append(sample.getId()).append(":0|1,1|0,1|1");
+                    sampleGenotypes.append(sample.getId()).append(":1|1");
+                }
+            }
+            samples = metadataManager.getSamples(
+                    metadataManager.getVariantMetadata().getStudies().get(0).getId());
+
+            // e.g.: sample genotypes = sample1:0|0;sample2:1|0,1|1
+            String[] values = sampleGenotypes.toString().split("[;]");
+            StringBuilder newSampleGenotypes = new StringBuilder();
+            if (values == null) {
+                newSampleGenotypes.append(updateSampleGenotype(sampleGenotypes.toString(), samples));
+            } else {
+                newSampleGenotypes.append(updateSampleGenotype(values[0], samples));
+                for (int i = 1; i < values.length; i++) {
+                    newSampleGenotypes.append(";");
+                    newSampleGenotypes.append(updateSampleGenotype(values[i], samples));
+                }
+            }
+            if (!StringUtils.isEmpty(newSampleGenotypes)) {
+                vd.sampleFilter("GT", newSampleGenotypes.toString());
+            } else {
+                System.err.format("Error: could not parse your sample genotypes %s.\n", sampleGenotypes);
+            }
+        }
+
+        // query for consequence type (Sequence Ontology term names and accession codes)
+        annotationFilterNotEmpty("consequenceTypes.sequenceOntologyTerms", filterParams.consequenceTypes, vd);
+
+        // query for consequence type (gene names)
+        annotationFilterNotEmpty("consequenceTypes.geneName", filterParams.genes, vd);
+
+        // query for clinvar (accession)
+        annotationFilterNotEmpty("variantTraitAssociation.clinvar.accession", filterParams.clinvar, vd);
+
+        // query for cosmic (mutation ID)
+        annotationFilterNotEmpty("variantTraitAssociation.cosmic.mutationId", filterParams.cosmic, vd);
+
+        // query for conservation (phastCons, phylop, gerp)
+        annotationFilterNotEmpty("conservation", filterParams.conservScores, vd);
+
+        // query for protein substitution scores (polyphen, sift)
+        annotationFilterNotEmpty("consequenceTypes.proteinVariantAnnotation.substitutionScores", filterParams.substScores, vd);
+
+        // query for alternate population frequency (study:population)
+        annotationFilterNotEmpty("populationFrequencies.altAlleleFreq", filterParams.pf, vd);
+
+        // query for population minor allele frequency (study:population)
+        annotationFilterNotEmpty("populationFrequencies.refAlleleFreq", filterParams.pmaf, vd);
+    }
+
+    private static void annotationFilterNotEmpty(String key, String value, VariantDataset vd) {
+        if (StringUtils.isNotEmpty(value)) {
+            vd.annotationFilter(key, value);
+        }
+    }
+
+    public static List<Region> getRegionList(String regions, String regionFilename) throws IOException {
+        List<Region> list = null;
+        if (StringUtils.isNotEmpty(regions)) {
+            list = Region.parseRegions(regions);
+        }
+        if (StringUtils.isNotEmpty(regionFilename) && new File(regionFilename).exists()) {
+            if (regions == null) {
+                list = new ArrayList<>();
+            }
+            List<String> lines = Files.readAllLines(Paths.get(regionFilename));
+            for (String line : lines) {
+                list.add(new Region(line));
+            }
+        }
+        return list;
+    }
+
+    /**
+     * Update the sample genotype query string by replacing the sample name by
+     * its sample order, e.g.: from sample2:1|0,1|1 to 32:1|0,1|1.
+     *
+     * @param sampleGenotype     Sample genotype query string
+     * @param samples            Sample list in the right order (to get the sample index)
+     * @return                   Updated sample genotype query string
+     */
+    private static String updateSampleGenotype(String sampleGenotype, List<Sample> samples) {
+        // e.g.: value = sample2:1|0,1|1
+        StringBuilder newSampleGenotype = new StringBuilder("");
+        String[] splits = sampleGenotype.split("[:]");
+        if (splits == null) {
+            // error
+            System.err.format("Error: invalid expresion %s for sample genotypes.\n", sampleGenotype);
+        } else {
+            boolean found = false;
+            // TODO: move this functionality to the VariantMetadataManager (from sample name to sample index)
+            for (int i = 0; i < samples.size(); i++) {
+                if (splits[0].equals(samples.get(i).getId())) {
+                    newSampleGenotype.append(i).append(":").append(splits[1]);
+                    found = true;
+                    break;
+                }
+            }
+            // Sanity check
+            if (!found) {
+                // error
+                System.err.format("Error: sample %s not found in dataset.\n", splits[0]);
+            }
+        }
+        System.out.println(sampleGenotype + " -> " + newSampleGenotype.toString());
+        return newSampleGenotype.toString();
+    }
+
+    /**
+     * Export variant metadata into pedigree file format.
+     *
+     * @param metaFilename  Variant metadata file name
+     * @param studyId       Study ID target
+     * @param pedFilename   Pedigree file name
+     * @throws IOException  IO exception
+     */
+    public static void exportPedigree(String metaFilename, String studyId, String pedFilename) throws IOException {
+        VariantMetadataManager metadataManager = new VariantMetadataManager();
+        metadataManager.load(Paths.get(metaFilename));
+        Pedigree pedigree = metadataManager.getPedigree(studyId);
+        PedigreeManager pedigreeManager = new PedigreeManager();
+        pedigreeManager.save(pedigree, Paths.get(pedFilename));
+    }
+}
diff --git a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/tools/adaptors/PlinkAdaptor.java b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/wrappers/PlinkWrapper.java
similarity index 89%
rename from hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/tools/adaptors/PlinkAdaptor.java
rename to hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/wrappers/PlinkWrapper.java
index 6579b403..6457b0d4 100644
--- a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/tools/adaptors/PlinkAdaptor.java
+++ b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/wrappers/PlinkWrapper.java
@@ -1,4 +1,4 @@
-package org.opencb.hpg.bigdata.analysis.tools.adaptors;
+package org.opencb.hpg.bigdata.analysis.variant.wrappers;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.ObjectReader;
@@ -14,6 +14,7 @@
 import org.opencb.hpg.bigdata.analysis.tools.Executor;
 import org.opencb.hpg.bigdata.analysis.tools.Status;
 import org.opencb.hpg.bigdata.analysis.tools.ToolManager;
+import org.opencb.hpg.bigdata.analysis.variant.VariantAnalysisExecutor;
 import org.opencb.hpg.bigdata.core.lib.SparkConfCreator;
 import org.opencb.hpg.bigdata.core.lib.VariantDataset;
 import org.slf4j.Logger;
@@ -24,19 +25,20 @@
 import java.util.HashMap;
 import java.util.Map;
 
-public class PlinkAdaptor {
+public class PlinkWrapper extends VariantAnalysisWrapper {
 
     private Query query;
     private QueryOptions queryOptions;
 
     private Logger logger;
 
-    public PlinkAdaptor() {
-        this.logger = LoggerFactory.getLogger(PlinkAdaptor.class);
+    public PlinkWrapper(String studyId) {
+        super(studyId);
+        this.logger = LoggerFactory.getLogger(PlinkWrapper.class);
     }
 
 
-    public void run() {
+    public void execute() {
 
         String inputAvroFilename = query.getString("input");
         String tmpVcfFilename = query.get("outdir") + "/tmp.vcf";
@@ -83,7 +85,7 @@ public void run() {
             //params.put("output", "/tmp/test.bam.bai");
 
             String commandLine = toolManager.createCommandLine("plink", "index", params);
-            System.out.println(commandLine);        Path tmp = Paths.get("/tmp");
+            System.out.println(commandLine);
 
             Executor.execute(commandLine, tmp, true);
 
diff --git a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/wrappers/RvTestsWrapper.java b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/wrappers/RvTestsWrapper.java
new file mode 100644
index 00000000..f61c728f
--- /dev/null
+++ b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/wrappers/RvTestsWrapper.java
@@ -0,0 +1,95 @@
+package org.opencb.hpg.bigdata.analysis.variant.wrappers;
+
+import org.opencb.hpg.bigdata.analysis.AnalysisExecutorException;
+import org.opencb.hpg.bigdata.analysis.exceptions.AnalysisToolException;
+import org.opencb.hpg.bigdata.analysis.tools.Executor;
+import org.opencb.hpg.bigdata.analysis.variant.FilterParameters;
+import org.opencb.hpg.bigdata.analysis.variant.VariantAnalysisExecutor;
+import org.opencb.hpg.bigdata.analysis.variant.VariantAnalysisUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.Map;
+
+/**
+ * Created by joaquin on 1/19/17.
+ */
+//public class RvTestsWrapper extends AnalysisExecutor implements Serializable {
+public class RvTestsWrapper extends VariantAnalysisWrapper { // extends AnalysisExecutor implements Serializable {
+    private String inFilename;
+    private String metaFilename;
+    private FilterParameters filterParams;
+    private Map<String, String> rvtestsParams;
+
+    private Logger logger;
+
+    public RvTestsWrapper(String studyId, String inFilename, String metaFilename,
+                          FilterParameters filterParams, Map<String, String> rvtestsParams) {
+        super(studyId);
+        this.inFilename = inFilename;
+        this.metaFilename = metaFilename;
+        this.filterParams = filterParams;
+        this.rvtestsParams = rvtestsParams;
+
+        this.logger = LoggerFactory.getLogger(PlinkWrapper.class);
+    }
+
+    @Override
+    public void execute() throws AnalysisExecutorException {
+        // Sanity chek
+        if (binPath == null || !binPath.toFile().exists()) {
+            String msg = "RvTests binary path is missing.";
+            logger.error("RvTests binary path is missing.");
+            throw new AnalysisExecutorException("RvTests binary path is missing.");
+        }
+
+        // Get output dir
+        Path outDir = Paths.get("/tmp");
+        if (rvtestsParams.get("out") != null) {
+            outDir = Paths.get(rvtestsParams.get("out")).getParent();
+        }
+
+        // Export target variants to VCF file
+        String vcfFilename = outDir.toString() + "/tmp.vcf";
+        VariantAnalysisUtils.exportVCF(inFilename, metaFilename, filterParams, vcfFilename);
+
+        // Export pedigree
+        String pedFilename = outDir.toString() + "/tmp.vcf.ped";
+        try {
+            VariantAnalysisUtils.exportPedigree(metaFilename, studyId, pedFilename);
+        } catch (IOException e) {
+            logger.error(e.getMessage());
+            throw new AnalysisExecutorException(e);
+        }
+
+        StringBuilder sb = new StringBuilder();
+/*
+        // Compress vcf to bgz
+        sb.setLength(0);
+        sb.append(BGZIP_BIN).append(" ").append(vcfFilename);
+        Executor.execute(sb.toString(), outDir, true);
+
+        // ...create tabix index
+        sb.setLength(0);
+        sb.append(TABIX_BIN).append(" -p vcf ").append(vcfFilename).append(".gz");
+        Executor.execute(sb.toString(), outDir, true);
+*/
+        // ...and finally, run rvtests
+        sb.setLength(0);
+        sb.append(binPath);
+        sb.append(" --inVcf ").append(vcfFilename).append(".gz");
+        sb.append(" --pheno ").append(pedFilename);
+        for (String key: rvtestsParams.keySet()) {
+            sb.append(" --").append(key).append(" ").append(rvtestsParams.get(key));
+        }
+        try {
+            Executor.execute(sb.toString(), outDir, true);
+        } catch (AnalysisToolException e) {
+            logger.error(e.getMessage());
+            throw new AnalysisExecutorException(e);
+        }
+    }
+}
diff --git a/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/wrappers/VariantAnalysisWrapper.java b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/wrappers/VariantAnalysisWrapper.java
new file mode 100644
index 00000000..c1d1228b
--- /dev/null
+++ b/hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/wrappers/VariantAnalysisWrapper.java
@@ -0,0 +1,22 @@
+package org.opencb.hpg.bigdata.analysis.variant.wrappers;
+
+import org.opencb.hpg.bigdata.analysis.variant.VariantAnalysisExecutor;
+
+import java.nio.file.Path;
+
+public abstract class VariantAnalysisWrapper extends VariantAnalysisExecutor {
+
+    protected Path binPath;
+
+    protected VariantAnalysisWrapper(String studyId) {
+        super(studyId);
+    }
+
+    public void setBinPath(Path binPath) {
+        this.binPath = binPath;
+    }
+
+    public Path getBinPath() {
+        return binPath;
+    }
+}
diff --git a/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/CliUtils.java b/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/CliUtils.java
index 37d2c702..75e06a02 100644
--- a/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/CliUtils.java
+++ b/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/CliUtils.java
@@ -43,6 +43,7 @@ public static String getOutputFilename(String input, String output, String to) t
         return res;
     }
 
+    @Deprecated
     public static List<Region> getRegionList(String regions, String regionFilename) throws IOException {
         List<Region> list = null;
         if (StringUtils.isNotEmpty(regions)) {
@@ -97,6 +98,7 @@ public static void saveDatasetAsOneFile(ParentDataset ds, String format, String
         dir.delete();
     }
 
+    @Deprecated
     public static void addVariantFilters(VariantCommandOptions variantCommandOptions,
                                          VariantDataset vd) throws IOException {
 
@@ -253,6 +255,7 @@ public static void addVariantFilters(VariantCommandOptions variantCommandOptions
                 variantCommandOptions.queryVariantCommandOptions.pmaf, vd);
     }
 
+    @Deprecated
     private static void annotationFilterNotEmpty(String key, String value, VariantDataset vd) {
         if (StringUtils.isNotEmpty(value)) {
             vd.annotationFilter(key, value);
@@ -282,6 +285,7 @@ public static VariantCommandOptions createVariantCommandOptions(
      * @param samples            Sample list in the right order (to get the sample index)
      * @return                   Updated sample genotype query string
      */
+    @Deprecated
     private static String updateSampleGenotype(String sampleGenotype, List<Sample> samples) {
         // e.g.: value = sample2:1|0,1|1
         StringBuilder newSampleGenotype = new StringBuilder("");
diff --git a/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/LocalCliOptionsParser.java b/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/LocalCliOptionsParser.java
index fe207e79..c31221c5 100644
--- a/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/LocalCliOptionsParser.java
+++ b/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/LocalCliOptionsParser.java
@@ -20,6 +20,7 @@
 import com.beust.jcommander.Parameter;
 import com.beust.jcommander.ParameterDescription;
 import com.beust.jcommander.ParameterException;
+import org.opencb.hpg.bigdata.analysis.variant.FilterParameters;
 import org.opencb.hpg.bigdata.app.cli.local.options.*;
 
 import java.util.Map;
@@ -35,6 +36,7 @@ public class LocalCliOptionsParser {
     private final CommandOptions commandOptions;
 
     private final CommonCommandOptions commonCommandOptions;
+    private final FilterParameters filterOptions;
 
     private AdminCommandOptions adminCommandOptions;
 
@@ -55,6 +57,7 @@ public LocalCliOptionsParser() {
 
         commandOptions = new CommandOptions();
         commonCommandOptions = new CommonCommandOptions();
+        filterOptions = new FilterParameters();
 
         adminCommandOptions = new AdminCommandOptions(commonCommandOptions, jcommander);
         jcommander.addCommand("admin", adminCommandOptions);
@@ -77,7 +80,7 @@ public LocalCliOptionsParser() {
         alignmentSubCommands.addCommand("coverage", alignmentCommandOptions.coverageAlignmentCommandOptions);
         alignmentSubCommands.addCommand("query", alignmentCommandOptions.queryAlignmentCommandOptions);
 
-        variantCommandOptions = new VariantCommandOptions(commonCommandOptions, jcommander);
+        variantCommandOptions = new VariantCommandOptions(commonCommandOptions, filterOptions, jcommander);
         jcommander.addCommand("variant", variantCommandOptions);
         JCommander variantSubCommands = jcommander.getCommands().get("variant");
         variantSubCommands.addCommand("convert", variantCommandOptions.convertVariantCommandOptions);
diff --git a/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/executors/VariantCommandExecutor.java b/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/executors/VariantCommandExecutor.java
index 3abe2138..940e3753 100644
--- a/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/executors/VariantCommandExecutor.java
+++ b/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/executors/VariantCommandExecutor.java
@@ -31,10 +31,10 @@
 import org.opencb.biodata.models.metadata.SampleSetType;
 import org.opencb.biodata.models.variant.avro.StudyEntry;
 import org.opencb.biodata.models.variant.avro.VariantAvro;
-import org.opencb.biodata.models.variant.avro.VariantFileMetadata;
+import org.opencb.biodata.models.variant.metadata.VariantFileMetadata;
 import org.opencb.biodata.tools.variant.metadata.VariantMetadataManager;
 import org.opencb.commons.utils.FileUtils;
-import org.opencb.hpg.bigdata.analysis.variant.RvTestsAdaptor;
+import org.opencb.hpg.bigdata.analysis.variant.wrappers.RvTestsWrapper;
 import org.opencb.hpg.bigdata.app.cli.CommandExecutor;
 import org.opencb.hpg.bigdata.app.cli.local.CliUtils;
 import org.opencb.hpg.bigdata.app.cli.local.options.VariantCommandOptions;
@@ -53,7 +53,7 @@
 
 import static java.nio.file.Paths.get;
 
-//import org.opencb.hpg.bigdata.analysis.variant.analysis.RvTestsAdaptor;
+//import org.opencb.hpg.bigdata.analysis.variant.analysis.RvTestsWrapper;
 
 /**
  * Created by imedina on 25/06/15.
@@ -193,7 +193,7 @@ private void convert() throws IOException {
                     ObjectMapper mapper = new ObjectMapper();
                     //mapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
                     VariantFileMetadata data = mapper.readValue(metaFile, VariantFileMetadata.class);
-                    data.setFileName(outMetaFile.toString());
+                    data.setId(outMetaFile.toString());
 
                     // write the metadata
                     PrintWriter writer = new PrintWriter(new FileOutputStream(outMetaFile));
@@ -371,6 +371,9 @@ public void metadata() throws Exception {
             if (variantCommandOptions.metadataVariantCommandOptions.loadPedFilename != null) {
                 Pedigree pedigree = new PedigreeManager().parse(
                         get(variantCommandOptions.metadataVariantCommandOptions.loadPedFilename));
+
+                System.out.println(pedigree.toString());
+
                 metadataManager.loadPedigree(pedigree, datasetId);
                 updated = true;
             }
@@ -418,12 +421,14 @@ public void metadata() throws Exception {
 
 
     public void rvtests() throws Exception {
-        RvTestsAdaptor rvtests = new RvTestsAdaptor(variantCommandOptions.rvtestsVariantCommandOptions.inFilename,
-                variantCommandOptions.rvtestsVariantCommandOptions.metaFilename,
-                variantCommandOptions.rvtestsVariantCommandOptions.outDirname,
-                variantCommandOptions.rvtestsVariantCommandOptions.confFilename);
-
-//        rvtests.run(variantCommandOptions.rvtestsVariantCommandOptions.datasetId);
-        rvtests.run00(variantCommandOptions.rvtestsVariantCommandOptions.datasetId);
+        RvTestsWrapper rvtests = new RvTestsWrapper(variantCommandOptions.rvtestsVariantCommandOptions.datasetId,
+                variantCommandOptions.rvtestsVariantCommandOptions.inFilename,
+                variantCommandOptions.rvtestsVariantCommandOptions.inFilename + ".meta.json",
+                variantCommandOptions.rvtestsVariantCommandOptions.filterParameters,
+                variantCommandOptions.rvtestsVariantCommandOptions.rvtestsParams);
+
+        // TODO: get the binary path from config folder
+        rvtests.setBinPath(Paths.get("/home/jtarraga/soft/rvtests/executable/rvtest"));
+        rvtests.execute();
     }
 }
diff --git a/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/options/VariantCommandOptions.java b/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/options/VariantCommandOptions.java
index 67a5b160..1b299923 100644
--- a/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/options/VariantCommandOptions.java
+++ b/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/options/VariantCommandOptions.java
@@ -1,12 +1,13 @@
 package org.opencb.hpg.bigdata.app.cli.local.options;
 
-import com.beust.jcommander.JCommander;
-import com.beust.jcommander.Parameter;
-import com.beust.jcommander.Parameters;
-import com.beust.jcommander.ParametersDelegate;
+import com.beust.jcommander.*;
 import org.apache.parquet.hadoop.ParquetWriter;
+import org.opencb.hpg.bigdata.analysis.variant.FilterParameters;
 import org.opencb.hpg.bigdata.app.cli.local.LocalCliOptionsParser;
 
+import java.util.HashMap;
+import java.util.Map;
+
 /**
  * Created by jtarraga on 01/06/17.
  */
@@ -23,6 +24,7 @@ public class VariantCommandOptions {
     public RvTestsVariantCommandOptions rvtestsVariantCommandOptions;
 
     public LocalCliOptionsParser.CommonCommandOptions commonCommandOptions;
+    public FilterParameters commonFilterOptions;
     public JCommander jCommander;
 
     public VariantCommandOptions(LocalCliOptionsParser.CommonCommandOptions commonCommandOptions,
@@ -38,6 +40,21 @@ public VariantCommandOptions(LocalCliOptionsParser.CommonCommandOptions commonCo
         this.rvtestsVariantCommandOptions = new RvTestsVariantCommandOptions();
     }
 
+    public VariantCommandOptions(LocalCliOptionsParser.CommonCommandOptions commonCommandOptions,
+                                 FilterParameters commonFilterOptions,
+                                 JCommander jCommander) {
+        this.commonCommandOptions = commonCommandOptions;
+        this.commonFilterOptions = commonFilterOptions;
+        this.jCommander = jCommander;
+
+        this.convertVariantCommandOptions = new ConvertVariantCommandOptions();
+        this.annotateVariantCommandOptions = new AnnotateVariantCommandOptions();
+        this.viewVariantCommandOptions = new ViewVariantCommandOptions();
+        this.queryVariantCommandOptions = new QueryVariantCommandOptions();
+        this.metadataVariantCommandOptions = new MetadataVariantCommandOptions();
+        this.rvtestsVariantCommandOptions = new RvTestsVariantCommandOptions();
+    }
+
     @Parameters(commandNames = {"convert"}, commandDescription = "Convert gVCF/VCF files to different big data"
             + " formats such as Avro and Parquet using OpenCB models")
     public class ConvertVariantCommandOptions {
@@ -331,10 +348,16 @@ public class RvTestsVariantCommandOptions {
         @ParametersDelegate
         public LocalCliOptionsParser.CommonCommandOptions commonOptions = commonCommandOptions;
 
+        @ParametersDelegate
+        public FilterParameters filterParameters = commonFilterOptions;
+
+        @Parameter(names = {"--dataset"}, description = "Target dataset.", arity = 1)
+        public String datasetId = null;
+
         @Parameter(names = {"-i", "--input"}, description = "Input file name (in Avro/Parquet file format).",
                 required = true, arity = 1)
         public String inFilename;
-
+/*
         @Parameter(names = {"-m", "--metadata"}, description = "Input metadata file name.",
                 required = true, arity = 1)
         public String metaFilename;
@@ -343,12 +366,8 @@ public class RvTestsVariantCommandOptions {
                 required = true, arity = 1)
         public String outDirname;
 
-        @Parameter(names = {"--dataset"}, description = "Target dataset.",
-                arity = 1)
-        public String datasetId = null;
-
-        @Parameter(names = {"-c", "--config"}, description = "Configuration file name containing the rvtests parameters.",
-                required = true, arity = 1)
-        public String confFilename;
+*/
+        @DynamicParameter(names = "-D", description = "RvTests parameters")
+        public Map<String, String> rvtestsParams = new HashMap<>();
     }
 }
diff --git a/hpg-bigdata-app/src/test/java/org/opencb/hpg/bigdata/app/cli/local/VariantRvTestsCLITest.java b/hpg-bigdata-app/src/test/java/org/opencb/hpg/bigdata/app/cli/local/VariantRvTestsCLITest.java
index 2a3e64b0..e25cd198 100644
--- a/hpg-bigdata-app/src/test/java/org/opencb/hpg/bigdata/app/cli/local/VariantRvTestsCLITest.java
+++ b/hpg-bigdata-app/src/test/java/org/opencb/hpg/bigdata/app/cli/local/VariantRvTestsCLITest.java
@@ -2,7 +2,6 @@
 
 import org.junit.Test;
 
-import java.net.URISyntaxException;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
@@ -10,36 +9,60 @@
  * Created by joaquin on 1/19/17.
  */
 public class VariantRvTestsCLITest {
-    Path inPath;
-    Path outPath;
-    Path confPath;
-
-    private void init() throws URISyntaxException {
-        String root = "/home/jtarraga/data100/vcf/rvtest-skat/spark";
-//        String root = "/home/jtarraga/data/vcf/skat/";
-        inPath = Paths.get(root + "/example.vcf.avro");
-        outPath = Paths.get(root + "/out");
-        confPath = Paths.get(root + "/skat.params");
+    String datasetName = "test";
+
+    String vcfFilename = "../hpg-bigdata-app/src/test/resources/example.vcf";
+    String phenoFilename = "../hpg-bigdata-app/src/test/resources/pheno";
+    String outDir = "/tmp/";
+
+    Path vcfPath;
+    Path phenoPath;
+    Path avroPath;
+    Path metaPath;
+
+    private void init() throws Exception {
+        vcfPath = Paths.get(vcfFilename);
+        phenoPath = Paths.get(phenoFilename);
+        avroPath = Paths.get(outDir + "/" + vcfPath.getFileName() + ".avro");
+        metaPath = Paths.get(outDir + "/" + vcfPath.getFileName() + ".avro.meta.json");
+
+        avroPath.toFile().delete();
+        metaPath.toFile().delete();
+
+        // convert vcf to avro
+        StringBuilder commandLine = new StringBuilder();
+        commandLine.append(" variant convert");
+        commandLine.append(" --log-level ERROR");
+        commandLine.append(" -i ").append(vcfPath);
+        commandLine.append(" -o ").append(avroPath);
+        commandLine.append(" --dataset ").append(datasetName);
+        VariantQueryCLITest.execute(commandLine.toString());
+
+        // load pedigree file
+        commandLine.setLength(0);
+        commandLine.append(" variant metadata");
+        commandLine.append(" --log-level ERROR");
+        commandLine.append(" -i ").append(avroPath);
+        commandLine.append(" --load-pedigree ").append(phenoPath);
+        commandLine.append(" --dataset ").append(datasetName);
+        VariantQueryCLITest.execute(commandLine.toString());
     }
 
     @Test
     public void skat() {
-
         try {
             init();
 
             StringBuilder commandLine = new StringBuilder();
             commandLine.append(" variant rvtests");
             commandLine.append(" --log-level ERROR");
-            commandLine.append(" -i ").append(inPath);
-            commandLine.append(" -o ").append(outPath);
-            commandLine.append(" -c ").append(confPath);
-            commandLine.append(" --dataset noname");
-
+            commandLine.append(" --dataset ").append(datasetName);
+            commandLine.append(" -i ").append(avroPath);
+            commandLine.append(" -Dsingle=wald");
+            commandLine.append(" -Dout=/tmp/out.wald");
             VariantQueryCLITest.execute(commandLine.toString());
         } catch (Exception e) {
             e.printStackTrace();
         }
     }
-
 }
diff --git a/hpg-bigdata-app/src/test/resources/example.vcf b/hpg-bigdata-app/src/test/resources/example.vcf
new file mode 100755
index 00000000..a2358409
--- /dev/null
+++ b/hpg-bigdata-app/src/test/resources/example.vcf
@@ -0,0 +1,9 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20140730
+##reference=ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
+##source=1000GenomesPhase3Pipeline
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	P1	P2	P3	P4	P5	P6	P7	P8	P9
+1	1	.	A	G	100	.	.	GT	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/0
+1	2	.	A	G	100	.	.	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1
+1	3	.	A	G	100	.	.	GT	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0
diff --git a/hpg-bigdata-app/src/test/resources/pheno b/hpg-bigdata-app/src/test/resources/pheno
new file mode 100755
index 00000000..608afd9b
--- /dev/null
+++ b/hpg-bigdata-app/src/test/resources/pheno
@@ -0,0 +1,10 @@
+#fid iid fatid matid sex phenotype y1 y2 y3 y4
+P1 P1 0 0 0 2 1.911 -1.465 -0.817 1
+P2 P2 0 0 2 2 2.146 -2.451 -0.178 2
+P3 P3 0 0 2 1 1.086 -1.194 -0.899 1
+P4 P4 0 0 2 1 0.704 -1.052 -0.237 1
+P5 P5 0 0 1 2 2.512 -3.085 -2.579 1
+P6 P6 0 0 2 2 1.283 -1.294 -0.342 1
+P7 P7 0 0 1 2 2.384 1.070 -1.522 2
+P8 P8 0 0 1 1 3.004 0.680 -1.875 1
+P9 P9 0 0 1 1 0.714 -0.116 -1.604 1