igv-reports

igv-reports - A Python application to generate self-contained HTML reports for variant review and other genomic applications. Reports consist of a table of genomic sites and an embedded IGV genome browser for viewing data for each site. The tool extracts slices of data for each site and embeds the data as blobs in the HTML report file. The report can be opened in a web browser as a static page, with no depenency on the original input files.

Installation

Prerequisites

igv-reports requires Python 3.8 or greater.

Installing igv-reports

pip install igv-reports

igv-reports requires the package pysam version 0.22.0 or greater, which should be installed automatically. However, on OSX this sometimes fails due to missing dependent libraries. This can be fixed following the procedure below, from the pysam docs;
"The recommended way to install pysam is through conda/bioconda. This will install pysam from the bioconda channel and automatically makes sure that dependencies are installed. Also, compilation flags will be set automatically, which will potentially save a lot of trouble on OS X."

conda config --add channels r
conda config --add channels bioconda
conda install pysam

Creating a report

Reports are created with the command line script create_report, or alternatively python igv_reports/report.py. Command line arguments are described below. Although --tracks is optional, a typical report will include at least an alignment track (BAM or CRAM) file from which the variants were called.

Arguments:

• Required

  • sites VCF, BED, MAF, BEDPE, or generic tab delimited file of genomic variant sites. Tabix indexed files are supported and strongly recommended for large files.
  • --fasta Reference fasta file; must be indexed. This argument should be ommited if --genome is used, otherwise it is required.
  • --genome An igv.js genome identifier (e.g. hg38). If supplied fasta, ideogram, and the default annotation track for the specified genome will be used.*

• The arguments begin, end, and sequence are required for a generic tab delimited sites file.

  • --begin INT. Column of start chromosomal position for sites file. Used for generic tab delimited input.
  • --end INT. Column of end chromosomal position for sites. Used for generic tab delimited input.
  • --sequence INT. Column of sequence (chromosome) name.

• Optional coordinate system flag for generic tab delimited sites file only

  • --zero_based Specify that the position in the sites file is 0-based (e.g. UCSC files) rather than 1-based. Default is false.

• Optional

  • --ideogram FILE. Ideogram file in UCSC cytoIdeo format. Useful when fasta is used to specify the reference.
  • --tracks LIST. Space-delimited list of track files, see below for supported formats. If both tracks and track-config are specified tracks will appear first by default.
  • --track-config FILE. File containing array of json configuration objects for igv.js tracks. See the igv.js wiki for more details. This option allows customization of track parameters. When using this option, the track url and indexURL properties should be set to the paths of the respective files.
  • --roi LIST. Space-delimited list of region-of-interest (ROI) files. See igv.js wiki.
  • --template FILE. HTML template file.
  • --output FILE. Output file name; default="igvjs_viewer.html".
  • --info-columns LIST. Space delimited list of info field names to include in the variant table. If sites is a VCF file these are the info ID values. If sites is a tab delimited format these are column names.
  • --info-columns-prefixes LIST. For VCF based reports only. Space delimited list of prefixes of VCF info field IDs to include in the variant table. Any info field with ID starting with one of the listed values will be included.
  • --samples LIST. Space delimited list of sample (i.e. genotypes) names. Used in conjunction with _ --sample-columns_.
  • --sample-columns LIST. Space delimited list of VCF sample FORMAT field names to include in the variant table. If --samples is specified columns will be restricted to those samples, otherwise all samples will be included.
  • --flanking INT. Genomic region to include either side of variant; default=1000.
  • --standalone Embed all JavaScript referenced via <script> tags in the page.
  • --sort Applies to alignment tracks only. If specified alignments are initally sorted by the specified option. Supported values include BASE, STRAND, INSERT_SIZE, MATE_CHR, and NONE. Default value is BASE for single nucleotide variants, NONE (no sorting) otherwise. See the igv.js documentation for more information.
  • --exclude-flags INT. Value is passed to samtools as "-F" flag. Used to filter alignments. Default value is 1536 which filters alignments marked "duplicate" or "vendor failed". To include all alignments use --exclude-flags 0. See samtools documentation for more details.
  • --idlink URL tempate for information link for VCF ID values. The token $$ will be substituted with the ID value. Example: --idlink 'https://www.ncbi.nlm.nih.gov/snp/?term=$$'
  • --no-embed Don't embed data. Fasta and track URLs are referenced unchanged. The resulting report is dependent on the original data files, which must be specified as URLs. Local files are not supported with this option.
  • --subsample FLOAT. Output only a portion of input alignments (0.0 -> 1.0). See samtools view documentation for more details
  • --maxlen INT. Maximum length of a variant (SV) to show in a single view. Variants exceeding this length will be shown in a split-screen (multilocus) view. default = 10000
  • --translate-sequence-track Three-frame Translate sequence track

Track file formats:

Currently supported track file formats are BAM, CRAM, VCF, BED, GFF3, GTF, WIG, and BEDGRAPH. FASTA. BAM, CRAM, and VCF
files must be indexed. Tabix is supported and it is recommended that all large files be indexed.

Examples

Data for the examples are available in the github repository https://github.com/igvteam/igv-reports. The repository can be downloaded as a zip archive here https://github.com/igvteam/igv-reports/archive/refs/heads/master.zip. It is assumed that the examples are run from the root directory of the repository. Output html is written to the examples directory.

Create a variant report from a VCF file: (Example output)

create_report test/data/variants/variants.vcf.gz \
--fasta https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa \
--ideogram test/data/hg38/cytoBandIdeo.txt \
--flanking 1000 \
--info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC \
--samples reads_1_fastq \
--sample-columns DP GQ \
--tracks test/data/variants/variants.vcf.gz test/data/variants/recalibrated.bam test/data/hg38/refGene.txt.gz \
--output example_vcf.html

Create a variant report from a BED file: (Example output)

echo bed
create_report test/data/variants/variants.bed \
--genome hg38 \
--flanking 1000 \
--info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC \
--tracks test/data/variants/variants.bed test/data/variants/recalibrated.bam \
--output example_genome.html

Create a variant report from a TCGA MAF file: (Example output)

create_report test/data/variants/tcga_test.maf \
--genome hg19 \
--flanking 1000 \
--info-columns Chromosome Start_position End_position Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS \
--tracks test/data/variants/tcga_test.maf \
--output example_maf.html

Create a variant report from a generic tab-delimited file: (Example output)

create_report test/data/variants/test.maflite.tsv \
--genome hg19 \
--sequence 1 --begin 2 --end 3 \
--flanking 1000 \
--info-columns chr start end ref_allele alt_allele \
--output example_tab.html

Create a structural variant report from a vcf file with CHR2 and END info fields: (Example output)

create_report test/data/variants/SKBR3_Sniffles_sv.vcf \
--genome hg19 \
--flanking 1000 \
--maxlen 10500 \
--info-columns SVLEN \
--tracks test/data/variants/SKBR3_Sniffles_sv.vcf https://igv-genepattern-org.s3.amazonaws.com/test/bam/reads_lr_skbr3.sampled.bam \
--output example_sv.html 

Create a structural variant report from a bedpe file with two locations (BEDPE format): (Example output)

create_report test/data/variants/SKBR3_Sniffles_tra.bedpe \
--genome hg19 \
--flanking 1000 \
--tracks test/data/variants/SKBR3_Sniffles_variants_tra.vcf test/data/variants/SKBR3.ill.bam \
--output example_bedpe.html

Create a report using a genome identifier: (Example output)

create_report test/data/variants/variants.vcf.gz \
--genome hg38 \
--flanking 1000 \
--info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC \
--tracks test/data/variants/variants.vcf.gz test/data/variants/recalibrated.bam \
--output example_genome.html

Create a variant report with tracks defined in an igv.js track config json file: (Example output)

create_report test/data/variants/variants.vcf.gz \
--fasta https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa \
--ideogram test/data/hg38/cytoBandIdeo.txt \
--flanking 1000 \
--info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC \
--track-config test/data/variants/trackConfigs.json \
--output example_config.html

Create a variant report with custom ID link urls: (Example output)

create_report test/data/variants/1kg_phase3_sites.vcf.gz \
--genome hg19 \
--flanking 1000 \
--tracks test/data/variants/1kg_phase3_sites.vcf.gz test/data/variants/NA12878_lowcoverage.bam \
--idlink 'https://www.ncbi.nlm.nih.gov/snp/?term=$$' \
--output example_idlink.html

Create a junction report from a splice-junction bed file: (Example output)

create_report test/data/junctions/Introns.38.bed \
--genome hg38 \
--type junction \
--track-config test/data/junctions/tracks.json \
--info-columns TCGA GTEx variant_name \
--title "Sample A" \
--output example_junctions.html

Create a fusion report from a Trinity fusion json file:

create_report test/data/fusion/igv.fusion_inspector_web.json \
--fasta test/data/fusion/igv.genome.fa  \
--template igv_reports/templates/fusion_template.html  \  
--track-config test/data/fusion/tracks.json  \
--output example_fusion.html

Create a report containing wig and bedgraph files

create_report test/data/wig/regions.bed \
--genome hg19 \
--exclude-flags 512 \
--tracks test/data/wig/ucsc.bedgraph test/data/wig/mixed_step.wig test/data/wig/variable_step.wig \
--output example_wig.html

Use of info-columns-prefixes option. Variant track only, no alignments. (Example output)

python igv_reports/report.py test/data/annotated_vcf/consensus.filtered.ann.vcf \
--genome hg19 \
--flanking 1000 \
--info-columns cosmic_gene \
--info-columns-prefixes clinvar \
--tracks test/data/annotated_vcf/consensus.filtered.ann.vcf \
--output example_ann.html 

Use --exclude-flags option to include duplicate alignments in report by specifying a samtools --exclude-flags value. Default value is 1536 which filters duplicates and vendor-failed reads.

create_report test/data/dups/dups.bed \
--genome hg19 \
--exclude-flags 512 \
--tracks test/data/dups/dups.bam \
--output example_dups.html

Use -no-embed option to use external URL references for tracks in the report.

create_report test/data/variants/variants.vcf.gz \
--genome hg38 \
--no-embed \
--tracks https://igv-genepattern-org.s3.amazonaws.com/test/reports/variants.vcf.gz https://igv-genepattern-org.s3.amazonaws.com/test/reports/recalibrated.bam \
--output example_noembed.html

Converting genomic files to data URIs for use in igv.js

The script create_datauri (python igv_reports/datauri.py) converts the contents of a file to a data uri for use in igv.js. The datauri will be printed to stdout. NOTE It is not neccessary to run this script explicitly to create a report, it is documented here for use with stand-alone igv.js.

Convert a gzipped vcf file to a datauri.

create_datauri test/data/variants/variants.vcf.gz

Convert a slice of a local bam file to a datauri.

create_datauri --region chr5:474,969-475,009 test/data/variants/recalibrated.bam 

Convert a remote bam file to a datauri.

create_datauri --region chr5:474,969-475,009 https://1000genomes.s3.amazonaws.com/phase3/data/NA12878/alignment/NA12878.mapped.ILLUMINA.bwa.CEU.low_coverage.20121211.bam

Release Notes