jvarkit

Biostar130456

Last commit

Split individual VCF files from multisamples VCF file

Usage

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

Usage: java -jar dist/jvarkit.jar biostar130456  [options] Files

Usage: biostar130456 [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
    --disable-vc-attribute-recalc
      When genotypes are removed/changed, Dd not recalculate variant 
      attributes like DP, AF, AC, AN...
      Default: false
    -f, --filtered
      remove filtered Genotype
      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].
    -z, --homref
      remove homzygote REF/REF
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
  * -p, --pattern
      output file pattern. Must contain the word __SAMPLE__
    -x, --uncalled
      remove uncalled genotypes
      Default: false
    --vc-attribute-recalc-ignore-filtered
      When recalculating variant attributes like DP AF, AC, AN, ignore 
      FILTERed **Genotypes**
      Default: false
    --vc-attribute-recalc-ignore-missing
      Ignore missing VCF headers (DP, AF, AC, AN). Default behavior: adding 
      VCF header if they're missing
      Default: false
    --version
      print version and exit

Keywords

vcf
samples
sample

Creation Date

20150210

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar130456.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/biostar/Biostar130456Test.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 biostar130456 ? 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

bash
$   curl -sL "https://raw.githubusercontent.com/arq5x/bedtools2/bc2f97d565c36a82c1a0b12f570fed4398001e5f/test/map/test.vcf" |\
    java -jar dist/biostar130456.jar -x -z -p "sample.__SAMPLE__.vcf.gz" 
sample.NA00003.vcf.gz
sample.NA00001.vcf.gz
sample.NA00002.vcf.gz

$ gunzip -c sample.NA00003.vcf.gz
(...)
##source=myImputationProgramV3.1
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00003
chr1	10	rs6054257	G	A	29	PASS	AF=0.5;DB;DP=14;H2;NS=3	GT:DP:GQ:HQ	1/1:5:43
chr1	20	rs6040355	A	G,T	67	PASS	AA=T;AF=0.333,0.667;DB;DP=10;NS=2	GT:DP:GQ	2/2:4:35
chr1	130	microsat1	GTC	G,GTCT	50	PASS	AA=G;DP=9;NS=3	GT:DP:GQ	1/1:3:40
chr2	130	microsat1	GTC	G,GTCT	50	PASS	AA=G;DP=9;NS=3	GT:DP:GQ	1/1:3:40