jvarkit

VcfMultiToOneAllele

‘one variant with N ALT alleles’ to ‘N variants with one ALT’

DEPRECATED

Use bcftools norm

Usage

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

Usage: java -jar dist/jvarkit.jar vcfmulti2oneallele  [options] Files

Usage: vcfmulti2oneallele [options] Files
  Options:
    --bcf-output
      If this program writes a VCF to a file, The format is first guessed from 
      the file suffix. Otherwise, force BCF output. The current supported BCF 
      version is : 2.1 which is not compatible with bcftools/htslib (last 
      checked 2019-11-15)
      Default: false
    -flag, --flag
      Info field name that will be added to recall the original alleles.
      Default: VCF_MULTIALLELIC_SRC
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --keepSpanningDeletions
      Keep Alt Spanning deletion alleles *
      Default: false
    --most-frequent
      Keep only most frequent allele.
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
    --print-no-alt
      Print Variants without ALT allele
      Default: false
    --version
      print version and exit

Keywords

• vcf

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfmulti2oneallele/VcfMultiToOneAllele.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 vcfmulti2oneallele ? 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

Deprecated

use bcftools norm

Example

Exac contains multi-ALT variants:

$ gunzip -c ExAC.r0.3.sites.vep.vcf.gz | grep rs3828049

1	889238	rs3828049	G	A,C	8422863.10	PASS	AC=6926,3;AC_AFR=220,0;AC_AMR=485,1;AC_Adj=6890,3;AC_EAS=746,0;AC_FIN=259,0;AC_Het=6442,3,0;AC_Hom=224,0;AC_NFE=3856,0;AC_OTH=41,0;AC_SAS=1283,2;AF=0.057,2.472e-05;AN=121358;AN_AFR=10148;AN_AMR=11522;AN_Adj=119272;AN_EAS=8582;AN_FIN=6358;AN_NFE=65282;AN_OTH=876;AN_SAS=16504;(...)

processed with this tools:

$ java -jar dist/jvarkit.jar vcfmulti2oneallele  ExAC.r0.3.sites.vep.vcf.gz   | grep rs3828049

1	889238	rs3828049	G	A	8422863.10	PASS	AC=6926;AC_AFR=220;AC_AMR=485;AC_Adj=6890;AC_EAS=746;AC_FIN=259;AC_Het=6442;AC_Hom=224;AC_NFE=3856;AC_OTH=41;AC_SAS=1283;AF=0.057;AN=121358;AN_AFR=10148;AN_AMR=11522;AN_Adj=119272;AN_EAS=8582;AN_FIN=6358;AN_NFE=65282;AN_OTH=876;AN_SAS=16504;BaseQRankSum=-2.170e-01;VCF_MULTIALLELIC_SRC=A|C;(...)
1	889238	rs3828049	G	C	8422863.10	PASS	AC=3;AC_AFR=0;AC_AMR=1;AC_Adj=3;AC_EAS=0;AC_FIN=0;AC_Het=3;AC_Hom=0;AC_NFE=0;AC_OTH=0;AC_SAS=2;AF=2.472e-05;AN=121358;AN_AFR=10148;AN_AMR=11522;AN_Adj=119272;AN_EAS=8582;AN_FIN=6358;AN_NFE=65282;AN_OTH=876;AN_SAS=16504;VCF_MULTIALLELIC_SRC=A|C;(....)

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