VcfForIGV

Prepare IGV sessions file and json for nextflow/igv_report

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar vcf4igv  [options] Files

Usage: vcf4igv [options] Files
  Options:
    --count
      For Case-controls (at least one 'case' and one 'control' in the 
      samplesheet' ) 8 comma integers representing the maximum number of bam 
      to display: case-HOM_REF,case-HET,case-HOM_VAR,case-NO_CALL,ctrl-HOM_REF,ctrl-HET,ctrl-HOM_VAR,ctr-NO_CALL 
      . A negative number is 'infinite'. If there is no case  4 comma 
      separated integers:HOM_REF,HET,HOM_VAR,NO_CALL (other fields are 
      ignored) 
      Default: 1,5,1,0,1,5,1,0
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
  * --samplesheet
      samplesheet. TSV or CSV file with the following header: 
      'bam,sample,status'. 'bam' is required, 'status' must be 'case' or 
      'control' 
    --session-dir
      if defined, save the IGV session XML files in that directory
    --version
      print version and exit

Keywords

• vcf
• igv
• json

Creation Date

20260506

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcf4igv/VcfForIGV.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcf4igv/VcfForIGVTest.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite vcf4igv ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Example

``` java -jar dist/jvarkit.jar vcf4igv -R src/test/resources/rotavirus_rf.fa --samplesheet jeter.csv src/test/resources/rotavirus_rf.vcf.gz | python3 -m json.tool

[ { "fasta": "/home/lindenb/src/jvarkit-git/src/test/resources/rotavirus_rf.fa", "interval": "RF01:970-970", "contig": "RF01", "chromosome": "RF01", "start": 970, "end": 970, "length": 1, "ref": "A", "alt": "C", "description": "RF01:970 CASE/HET:N=0. CASE/HOM_VAR:N=1 displayed here: S5. CASE/HOM_REF:N=2 displayed here: S1. CTRL/HET:N=0. CTRL/HOM_VAR=0. CTRL/HOM_REF:N=2 displayed here: S2. ", "bams": [ { "sample": "S5", "bam": "src/test/resources/S5.bam", "status": "case" }, { "sample": "S1", "bam": "src/test/resources/S1.bam", "status": "case" }, { "sample": "S2", "bam": "src/test/resources/S2.bam", "status": "control" } ] }, (...) ```