GATK CNV

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diff --git a/Manual/GATK_CNV.md b/Manual/GATK_CNV.md
diff --git a/Manual0/16S_history.md b/Manual0/16S_history.md
diff --git a/Manual0/16S_rRNA_gene_database.md b/Manual0/16S_rRNA_gene_database.md
diff --git a/Manual0/Annovar.md b/Manual0/Annovar.md
diff --git a/Manual0/BaiduPCS-Go.md b/Manual0/BaiduPCS-Go.md
diff --git a/Manual0/Binsanity.md b/Manual0/Binsanity.md
diff --git a/Manual0/CNCI.md b/Manual0/CNCI.md
diff --git a/Manual0/COG.md b/Manual0/COG.md
diff --git a/Manual0/COG_manual.md b/Manual0/COG_manual.md
diff --git a/Manual0/CONCOCT.md b/Manual0/CONCOCT.md
diff --git a/Manual0/CRISPR.md b/Manual0/CRISPR.md
diff --git a/Manual0/C_library.md b/Manual0/C_library.md
diff --git a/Manual0/CallSNV_FAQ.md b/Manual0/CallSNV_FAQ.md
diff --git a/Manual0/Centrifuge.md b/Manual0/Centrifuge.md
diff --git a/Manual0/CheckM.md b/Manual0/CheckM.md
diff --git a/Manual0/DaPars.md b/Manual0/DaPars.md
diff --git a/Manual0/FREEC.md b/Manual0/FREEC.md
diff --git a/Manual0/GDC_TCGA.md b/Manual0/GDC_TCGA.md
diff --git a/Manual0/GO_compare.md b/Manual0/GO_compare.md
diff --git a/Manual0/G_Statistics_for_BSA.md b/Manual0/G_Statistics_for_BSA.md
diff --git a/Manual0/GenomeTools.md b/Manual0/GenomeTools.md
diff --git a/Manual0/GraPhlAn.md b/Manual0/GraPhlAn.md
diff --git a/Manual0/HTSeq.md b/Manual0/HTSeq.md
diff --git a/Manual0/Infernal.md b/Manual0/Infernal.md
diff --git a/Manual0/KmerGenie.md b/Manual0/KmerGenie.md
diff --git a/Manual0/LTR_retriever.md b/Manual0/LTR_retriever.md
diff --git a/Manual0/LTRharvest.md b/Manual0/LTRharvest.md
diff --git a/Manual0/MACS.md b/Manual0/MACS.md
diff --git a/Manual0/MCScanX/MCScanX.md b/Manual0/MCScanX/MCScanX.md
diff --git a/Manual0/MCScanX/data/circle.ctl b/Manual0/MCScanX/data/circle.ctl
diff --git a/Manual0/MCScanX/data/dual_synteny.ctl b/Manual0/MCScanX/data/dual_synteny.ctl
diff --git a/Manual0/MCScanX/data/os_sb.blast b/Manual0/MCScanX/data/os_sb.blast
diff --git a/Manual0/MCScanX/data/os_sb.collinearity b/Manual0/MCScanX/data/os_sb.collinearity
diff --git a/Manual0/MCScanX/data/os_sb.control b/Manual0/MCScanX/data/os_sb.control
diff --git a/Manual0/MCScanX/data/os_sb.gff b/Manual0/MCScanX/data/os_sb.gff
diff --git a/Manual0/MCScanX/picture/os_sb.bar_plot.png b/Manual0/MCScanX/picture/os_sb.bar_plot.png
diff --git a/Manual0/MCScanX/picture/os_sb.circle.png b/Manual0/MCScanX/picture/os_sb.circle.png
diff --git a/Manual0/MCScanX/picture/os_sb.dot.png b/Manual0/MCScanX/picture/os_sb.dot.png
diff --git a/Manual0/MCScanX/picture/os_sb.dual.synteny.png b/Manual0/MCScanX/picture/os_sb.dual.synteny.png
diff --git a/Manual0/MCScanX/picture/syn_html.png b/Manual0/MCScanX/picture/syn_html.png
diff --git a/Manual0/MECAT.md b/Manual0/MECAT.md
diff --git a/Manual0/MISA.md b/Manual0/MISA.md
diff --git a/Manual0/MOCAT2.md b/Manual0/MOCAT2.md
diff --git a/Manual0/MetAML.md b/Manual0/MetAML.md
diff --git a/Manual0/MetaMLST.md b/Manual0/MetaMLST.md
diff --git a/Manual0/MetaPhlAn.md b/Manual0/MetaPhlAn.md
diff --git a/Manual0/Mutiple_sequence_alignment.md b/Manual0/Mutiple_sequence_alignment.md
diff --git a/Manual0/Nanopore_QC.md b/Manual0/Nanopore_QC.md
diff --git a/Manual0/PICRUSt.md b/Manual0/PICRUSt.md
diff --git a/Manual0/PILER.md b/Manual0/PILER.md
diff --git a/Manual0/PanPhlAn.md b/Manual0/PanPhlAn.md
diff --git a/Manual0/Pfam.md b/Manual0/Pfam.md
diff --git a/Manual0/PhyloCSF.md b/Manual0/PhyloCSF.md
diff --git a/Manual0/Prokka.md b/Manual0/Prokka.md
diff --git a/Manual0/RDA_analysis.md b/Manual0/RDA_analysis.md
diff --git a/Manual0/README.md b/Manual0/README.md
diff --git a/Manual0/RNA_variant.md b/Manual0/RNA_variant.md
diff --git a/Manual0/RSeQC.md b/Manual0/RSeQC.md
diff --git a/Manual0/R_library.md b/Manual0/R_library.md
diff --git a/Manual0/RepeatModeler.md b/Manual0/RepeatModeler.md
diff --git a/Manual0/SILVA_error.md b/Manual0/SILVA_error.md
diff --git a/Manual0/SPAdes.md b/Manual0/SPAdes.md
diff --git a/Manual0/SQLite.md b/Manual0/SQLite.md
diff --git a/Manual0/STAMP.md b/Manual0/STAMP.md
diff --git a/Manual0/STAMP/STAMP_interface.md b/Manual0/STAMP/STAMP_interface.md
diff --git a/Manual0/STAMP/pictures/analysis.png b/Manual0/STAMP/pictures/analysis.png
diff --git a/Manual0/STAMP/pictures/data.png b/Manual0/STAMP/pictures/data.png
diff --git a/Manual0/STAMP/pictures/group.png b/Manual0/STAMP/pictures/group.png
diff --git a/Manual0/STAMP/pictures/legend.png b/Manual0/STAMP/pictures/legend.png
diff --git a/Manual0/STAMP/pictures/loading_data.png b/Manual0/STAMP/pictures/loading_data.png
diff --git a/Manual0/STAMP/pictures/result.png b/Manual0/STAMP/pictures/result.png
diff --git a/Manual0/STAMP/pictures/save.png b/Manual0/STAMP/pictures/save.png
diff --git a/Manual0/STAR.md b/Manual0/STAR.md
diff --git a/Manual0/SURVIVOR.md b/Manual0/SURVIVOR.md
diff --git a/Manual0/SignaIP.md b/Manual0/SignaIP.md
diff --git a/Manual0/StrainPhlAn.md b/Manual0/StrainPhlAn.md
diff --git a/Manual0/TACO.md b/Manual0/TACO.md
diff --git a/Manual0/Taxonomy_classification.md b/Manual0/Taxonomy_classification.md
diff --git a/Manual0/Trim_adapters/Trim_adapters.md b/Manual0/Trim_adapters/Trim_adapters.md
diff --git a/Manual0/Trim_adapters/picture/1_raw.png b/Manual0/Trim_adapters/picture/1_raw.png
diff --git a/Manual0/Trim_adapters/picture/2_SOAPnuke.png b/Manual0/Trim_adapters/picture/2_SOAPnuke.png
diff --git a/Manual0/Trim_adapters/picture/2_fastp.png b/Manual0/Trim_adapters/picture/2_fastp.png
diff --git a/Manual0/Trim_adapters/picture/3_SOAPnuke.png b/Manual0/Trim_adapters/picture/3_SOAPnuke.png
diff --git a/Manual0/Trim_adapters/picture/3_SOAPnuke_untrim.png b/Manual0/Trim_adapters/picture/3_SOAPnuke_untrim.png
diff --git a/Manual0/Trim_adapters/picture/3_fastp.png b/Manual0/Trim_adapters/picture/3_fastp.png
diff --git a/Manual0/Trim_adapters/picture/R1_read.png b/Manual0/Trim_adapters/picture/R1_read.png
diff --git a/Manual0/Trim_adapters/picture/SOAPnuke.png b/Manual0/Trim_adapters/picture/SOAPnuke.png
diff --git a/Manual0/Trim_adapters/picture/SOAPnuke_trim.png b/Manual0/Trim_adapters/picture/SOAPnuke_trim.png
diff --git a/Manual0/Trim_adapters/picture/compare.png b/Manual0/Trim_adapters/picture/compare.png
diff --git a/Manual0/Trim_adapters/picture/cutadapt.png b/Manual0/Trim_adapters/picture/cutadapt.png
diff --git a/Manual0/Trim_adapters/picture/fastp.png b/Manual0/Trim_adapters/picture/fastp.png
diff --git a/Manual0/Trim_adapters/picture/fastp_trim.png b/Manual0/Trim_adapters/picture/fastp_trim.png
diff --git a/Manual0/Trim_adapters/picture/raw_R1.png b/Manual0/Trim_adapters/picture/raw_R1.png
diff --git a/Manual0/Trim_adapters/picture/raw_R2.png b/Manual0/Trim_adapters/picture/raw_R2.png
diff --git a/Manual0/Trim_adapters/picture/test_data.png b/Manual0/Trim_adapters/picture/test_data.png
diff --git a/Manual0/Trim_adapters/test_data/trim_test.R1.fq b/Manual0/Trim_adapters/test_data/trim_test.R1.fq
diff --git a/Manual0/Trim_adapters/test_data/trim_test.R2.fq b/Manual0/Trim_adapters/test_data/trim_test.R2.fq
diff --git a/Manual0/Trim_adapters/test_data/trim_test_SOAPnuke.R1.fq b/Manual0/Trim_adapters/test_data/trim_test_SOAPnuke.R1.fq
diff --git a/Manual0/Trim_adapters/test_data/trim_test_SOAPnuke.R2.fq b/Manual0/Trim_adapters/test_data/trim_test_SOAPnuke.R2.fq
diff --git a/Manual0/Trim_adapters/test_data/trim_test_cutadapt.R1.fq b/Manual0/Trim_adapters/test_data/trim_test_cutadapt.R1.fq
diff --git a/Manual0/Trim_adapters/test_data/trim_test_cutadapt.R2.fq b/Manual0/Trim_adapters/test_data/trim_test_cutadapt.R2.fq
diff --git a/Manual0/Trim_adapters/test_data/trim_test_fastp.R1.fq b/Manual0/Trim_adapters/test_data/trim_test_fastp.R1.fq
diff --git a/Manual0/Trim_adapters/test_data/trim_test_fastp.R2.fq b/Manual0/Trim_adapters/test_data/trim_test_fastp.R2.fq
diff --git a/Manual0/UID16S_report.md b/Manual0/UID16S_report.md
diff --git a/Manual0/UMI_TCR.md b/Manual0/UMI_TCR.md
diff --git a/Manual0/Ubuntu.md b/Manual0/Ubuntu.md
diff --git a/Manual0/ViennaRNA.md b/Manual0/ViennaRNA.md
diff --git a/Manual0/adonis_anosim.md b/Manual0/adonis_anosim.md
diff --git a/Manual0/alignment_tools.md b/Manual0/alignment_tools.md
diff --git a/Manual0/anaconda.md b/Manual0/anaconda.md
@@ -90,3 +90,22 @@ $ conda update anaconda
 # 更新python
 $ conda update python
 ```
+
+
+### export config file
+```
+$ conda env export > NanoSV.yaml
+````
+
+
+#### create environment based on the config file
+```
+conda env create -f environment.yml
+```
+
+set the installed pathway
+```
+conda env create -f environment.yml -p /home/user/anaconda3/envs/env_name
+```
+
+
diff --git a/Manual0/anvi.md b/Manual0/anvi.md
diff --git a/Manual0/aspera.md b/Manual0/aspera.md
diff --git a/Manual0/assembly_nanopore.md b/Manual0/assembly_nanopore.md
diff --git a/Manual0/assembly_tools.md b/Manual0/assembly_tools.md
diff --git a/Manual0/augustus.md b/Manual0/augustus.md
diff --git a/Manual0/bamFlagReads.md b/Manual0/bamFlagReads.md
diff --git a/Manual0/bamFlagReads.md.0 b/Manual0/bamFlagReads.md.0
diff --git a/Manual0/bedtools.md b/Manual0/bedtools.md
diff --git a/Manual0/blast.md b/Manual0/blast.md
diff --git a/Manual0/blast_diamond.md b/Manual0/blast_diamond.md
diff --git a/Manual0/busco.md b/Manual0/busco.md
diff --git a/Manual0/canu.md b/Manual0/canu.md
diff --git a/Manual0/cazy_db.md b/Manual0/cazy_db.md
diff --git a/Manual0/cd-hit.md b/Manual0/cd-hit.md
diff --git a/Manual0/circos.md b/Manual0/circos.md
diff --git a/Manual0/cnvkit.md b/Manual0/cnvkit.md
diff --git a/Manual0/database.md b/Manual0/database.md
diff --git a/Manual0/deeptools.md b/Manual0/deeptools.md
diff --git a/Manual0/delly.md b/Manual0/delly.md
diff --git a/Manual0/denovoVariant/Triodenovo.md b/Manual0/denovoVariant/Triodenovo.md
diff --git a/Manual0/denovoVariant/denovoVariant.md b/Manual0/denovoVariant/denovoVariant.md
diff --git a/Manual0/denovoVariant/denovogear.md b/Manual0/denovoVariant/denovogear.md
diff --git a/Manual0/docker_bio.md b/Manual0/docker_bio.md
diff --git a/Manual0/docker_general.md b/Manual0/docker_general.md
diff --git a/Manual0/docker_image.md b/Manual0/docker_image.md
diff --git a/Manual0/download_SRA_project.md b/Manual0/download_SRA_project.md
diff --git a/Manual0/eggnog-mapper.md b/Manual0/eggnog-mapper.md
diff --git a/Manual0/ensemble_genome.md b/Manual0/ensemble_genome.md
diff --git a/Manual0/falcon.md b/Manual0/falcon.md
diff --git a/Manual0/gaf_format.md b/Manual0/gaf_format.md
diff --git a/Manual0/gene_annotation.md b/Manual0/gene_annotation.md
diff --git a/Manual0/gene_ontology.md b/Manual0/gene_ontology.md
diff --git a/Manual0/git_manual.md b/Manual0/git_manual.md
diff --git a/Manual0/greengenes.md b/Manual0/greengenes.md
diff --git a/Manual0/hexo.md b/Manual0/hexo.md
diff --git a/Manual0/hexo_markdown_math.md b/Manual0/hexo_markdown_math.md
diff --git a/Manual0/hmmer.md b/Manual0/hmmer.md
diff --git a/Manual0/hmmsearch.md b/Manual0/hmmsearch.md
diff --git a/Manual0/humann2.md b/Manual0/humann2.md
diff --git a/Manual0/idmapping_db.md b/Manual0/idmapping_db.md
diff --git a/Manual0/japsa.md b/Manual0/japsa.md
diff --git a/Manual0/jcvi.md b/Manual0/jcvi.md
diff --git a/Manual0/jellyfish.md b/Manual0/jellyfish.md
diff --git a/Manual0/jupyter.md b/Manual0/jupyter.md
diff --git a/Manual0/jvarkit.md b/Manual0/jvarkit.md
diff --git a/Manual0/kaiju_krona.md b/Manual0/kaiju_krona.md
diff --git a/Manual0/kegg_db.md b/Manual0/kegg_db.md
diff --git a/Manual0/kneaddata.md b/Manual0/kneaddata.md
diff --git a/Manual0/lastz.md b/Manual0/lastz.md
diff --git a/Manual0/linux_general.md b/Manual0/linux_general.md
diff --git a/Manual0/lordfast.md b/Manual0/lordfast.md
diff --git a/Manual0/mafft.md b/Manual0/mafft.md
diff --git a/Manual0/manta.md b/Manual0/manta.md
diff --git a/Manual0/maxbin.md b/Manual0/maxbin.md
diff --git a/Manual0/megahit.md b/Manual0/megahit.md
diff --git a/Manual0/merge_PE_fastq.md b/Manual0/merge_PE_fastq.md
diff --git a/Manual0/metabat.md b/Manual0/metabat.md
diff --git a/Manual0/metaphyler.md b/Manual0/metaphyler.md
diff --git a/Manual0/metaquast.md b/Manual0/metaquast.md
diff --git a/Manual0/minimap2.md b/Manual0/minimap2.md
diff --git a/Manual0/mosdepth.md b/Manual0/mosdepth.md
diff --git a/Manual0/mothur.md b/Manual0/mothur.md
diff --git a/Manual0/mummer.md b/Manual0/mummer.md
diff --git a/Manual0/mysql.md b/Manual0/mysql.md
diff --git a/Manual0/mysql_ZFC.md b/Manual0/mysql_ZFC.md
diff --git a/Manual0/nanopack.md b/Manual0/nanopack.md
diff --git a/Manual0/ngmlr.md b/Manual0/ngmlr.md
diff --git a/Manual0/orthomcl.md b/Manual0/orthomcl.md
diff --git a/Manual0/parallel.md b/Manual0/parallel.md
diff --git a/Manual0/pblat.md b/Manual0/pblat.md
diff --git a/Manual0/pbs.md b/Manual0/pbs.md
diff --git a/Manual0/perl_general.md b/Manual0/perl_general.md
diff --git a/Manual0/pigz.md b/Manual0/pigz.md
diff --git a/Manual0/prefetch.md b/Manual0/prefetch.md
diff --git a/Manual0/prodigal.md b/Manual0/prodigal.md
diff --git a/Manual0/protein_database.md b/Manual0/protein_database.md
diff --git a/Manual0/pynast_FastTree.md b/Manual0/pynast_FastTree.md
diff --git a/Manual0/python_code.md b/Manual0/python_code.md
diff --git a/Manual0/qiime_workflow.md b/Manual0/qiime_workflow.md
diff --git a/Manual0/quast.md b/Manual0/quast.md
diff --git a/Manual0/repeatscout.md b/Manual0/repeatscout.md
diff --git a/Manual0/reports.md b/Manual0/reports.md
diff --git a/Manual0/rmats.md b/Manual0/rmats.md
diff --git a/Manual0/salmon.md b/Manual0/salmon.md
diff --git a/Manual0/samtools.md b/Manual0/samtools.md
@@ -82,6 +82,14 @@ samtools markdup in.algnsorted.bam out.bam
 ```
 
 
+### Extraction of unaligned reads (and mates) via samtools, per sample
+```
+samtools fastq –f 12 [alignments.bam] -1 [mateUnmapped_R1.fq] -2 [mateUnmapped_R2.fq]
+samtools fastq –f 68 –F 8 [alignments.bam] > [R1_mateMapped.fq]
+samtools fastq –f 132 –F 8 [alignments.bam] > [R2_mateMapped.fq]
+samtools view –f 8 –F 4 [alignments.bam] > [GRCh38Links.bam]
+```
+
 
 
 ### samtools mpileup

diff --git a/Manual0/sentieon.md b/Manual0/sentieon.md
diff --git a/Manual0/seq_tools.md b/Manual0/seq_tools.md
diff --git a/Manual0/seqkit_for_FREEC.md b/Manual0/seqkit_for_FREEC.md
diff --git a/Manual0/sniffles.md b/Manual0/sniffles.md
diff --git a/Manual0/snpEff.md b/Manual0/snpEff.md
diff --git a/Manual0/soapfuse.md b/Manual0/soapfuse.md
diff --git a/Manual0/sourmash.md b/Manual0/sourmash.md
diff --git a/Manual0/sphinx.md b/Manual0/sphinx.md
diff --git a/Manual0/structural_variation.md b/Manual0/structural_variation.md
diff --git a/Manual0/tRNA.md b/Manual0/tRNA.md
diff --git a/Manual0/taxonomy.md b/Manual0/taxonomy.md
diff --git a/Manual0/usearch.md b/Manual0/usearch.md
diff --git a/Manual0/variant_calling.md b/Manual0/variant_calling.md
diff --git a/Manual0/vcfstats.md b/Manual0/vcfstats.md
diff --git a/Manual0/vcftools.md b/Manual0/vcftools.md
diff --git a/Manual0/vsearch.md b/Manual0/vsearch.md
diff --git a/Manual0/xlsx2csv.md b/Manual0/xlsx2csv.md