VCFFlatten

Last commit

Flatten variants to one variant

Usage

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

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

Usage: vcfflatten [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
    --gene-extractor
      Activate default gene extractors. Variant will be grouped by gene using 
      snpeff/bcftools/vep annotations
      Default: false
    --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].
    -i, --id
      Default Variant ID
      Default: FLATTEN_VARIANT
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

vcf
burden
contrast

Creation Date

20230222

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfflatten/VCFFlatten.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 vcfflatten ? 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

Motivation

flatten all variants to one variant. At the end, a Sample will be set to 1/1 if one or more of his Genotypes in the VCF is contains an NON-(REF|NO_CALL) allele The idea is to use the VCF output of this tool in order to pipe it into bcftools contrast: we'll get a p-value for the whole VCF

Example

$ java -jar dist/jvarkit.jar vcfflatten --gene-extractor src/test/resources/rotavirus_rf.ann.vcf.gz 2> /dev/null 
##fileformat=VCFv4.2
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=MULTIPLE_CONTIG,Number=0,Type=Flag,Description="Record spans multiple chromosomes. Only first chromosome is reported">
##INFO=<ID=N_VARIANTS,Number=1,Type=Integer,Description="Number of variants">
(...)
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  S1  S2  S3  S4  S5
RF01    970 .   N   <FLATTEN_VARIANT>   .   .   MULTIPLE_CONTIG;N_VARIANTS=45   GT  1/1 1/1 1/1 1/1 1/1
RF01    970 .   N   <ANN/GeneName:Gene_18_3284> .   .   N_VARIANTS=1    GT  0/0 0/0 0/0 0/0 1/1
RF01    970 .   N   <ANN/FeatureId:AAA47319.1>  .   .   N_VARIANTS=1    GT  0/0 0/0 0/0 0/0 1/1
RF01    970 .   N   <ANN/GeneId:Gene_18_3284>   .   .   N_VARIANTS=1    GT  0/0 0/0 0/0 0/0 1/1
RF02    1962    .   N   <ANN/GeneId:UniProtKB/Swiss-Prot:P12472>    .   .   END=251;N_VARIANTS=5    GT  1/1 1/1 1/1 1/1 0/0
RF02    1962    .   N   <ANN/FeatureId:CAA32215.1>  .   .   END=251;N_VARIANTS=5    GT  1/1 1/1 1/1 1/1 0/0
RF02    1962    .   N   <ANN/FeatureId:CAA32213.1>  .   .   END=251;N_VARIANTS=5    GT  1/1 1/1 1/1 1/1 0/0
RF02    1962    .   N   <ANN/GeneName:Gene_1621_1636>   .   .   END=251;N_VARIANTS=5    GT  1/1 1/1 1/1 1/1 0/0