jvarkit

FindAVariation

Finds a specific mutation in a list of VCF files

Usage

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

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

Usage: findavariation [options] Files
  Options:
    --bcf
      Enable BCF. On 20200217 the java library htsjdk doesn't support the 
      recent version of bcf. This tool will call `bcftools` to get the 
      variants. bcftools must be in the ${PATH}.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -homref, --homref
      Hide HOM_REF genotypes
      Default: false
    -indexed, --indexed
      [20171020] Search only in indexed vcf
      Default: false
    -nocall, --nocall
      Hide NO_CALL genotypes
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
    -f, --posfile
      Add this file containing chrom:position
      Default: []
    -p, --position
      A list of 'chrom/position'
      Default: []
    -snp, --snp
      Search only variant have the very same position (ignore overlapping 
      variants) 
      Default: false
    --version
      print version and exit

Keywords

• vcf
• variation
• search
• find
• bcf

Creation Date

20140623

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/FindAVariation.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/FindAVariationTest.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 findavariation ? 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

$ find ./ -name "*.vcf" -o -name "*.vcf.gz" |\
   java -jar dist/findavariation.jar -p "chr1:1234" 


htsjdk/testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf	1	8216713	8216713	yossi-1		NA12878	HET	A G
htsjdk/testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf	1	8216713	8216713	yossi-1		NA12891	HET	A G
htsjdk/testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf	1	8216713	8216713	yossi-1		NA12892	HET	A G
htsjdk/testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf	2	2	2	.		NA12878	HOM_REF	C C
htsjdk/testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf	2	2	2	.		NA12891	HET	C T
htsjdk/testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf	2	2	2	.		NA12892	HET	C T

History

• 20180914 : replace DP4 with AD

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