jvarkit

VcfMultiToOne

Last commit

Convert VCF with multiple samples to a VCF with one SAMPLE, duplicating variant and adding the sample name in the INFO column.

Usage

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

Usage: java -jar dist/jvarkit.jar vcfmulti2one  [options] Files

Usage: vcfmulti2one [options] Files
  Options:
    --anonymize, -x
      anonymize samples
      Default: false
    --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
    -r, --hr, -hr, --discard_hom_ref
      discard if variant is hom-ref
      Default: false
    -c, --nc, -nc, --discard_no_call
      discard if variant is no-call
      Default: false
    -a, --discard_non_available
      discard if variant is not available (see htsjdk definition 'available if 
      the type of this genotype is set')
      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].
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

vcf
sample

Creation Date

20150312

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfmulti2one/VcfMultiToOne.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfmulti2one/VcfMultiToOneTest.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 vcfmulti2one ? 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

Input

if there is only one input with the ‘.list’ suffix, it is interpreted as a file containing the path to the vcf files

$ curl -s "http://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz" |\
gunzip -c |\
java -jar dist/jvarkit.jar vcfmulti2one  -c -r -a  |\
grep -v '##' |\
grep -E '(CHROM|SAMPLENAME)' | head | verticalize 


>>> 2
$1   #CHROM : 1
$2      POS : 10177
$3       ID : .
$4      REF : A
$5      ALT : AC
$6     QUAL : 100
$7   FILTER : PASS
$8     INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00096;SAS_AF=0
.4949
$9   FORMAT : GT
$10  SAMPLE : 1|0
<<< 2

>>> 3
$1   #CHROM : 1
$2      POS : 10177
$3       ID : .
$4      REF : A
$5      ALT : AC
$6     QUAL : 100
$7   FILTER : PASS
$8     INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00097;SAS_AF=0
.4949
$9   FORMAT : GT
$10  SAMPLE : 0|1
<<< 3

>>> 4
$1   #CHROM : 1
$2      POS : 10177
$3       ID : .
$4      REF : A
$5      ALT : AC
$6     QUAL : 100
$7   FILTER : PASS
$8     INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00099;SAS_AF=0
.4949
$9   FORMAT : GT
$10  SAMPLE : 0|1
<<< 4

>>> 5
$1   #CHROM : 1
$2      POS : 10177
$3       ID : .
$4      REF : A
$5      ALT : AC
$6     QUAL : 100
$7   FILTER : PASS
$8     INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00100;SAS_AF=0
.4949
$9   FORMAT : GT
$10  SAMPLE : 1|0
<<< 5

>>> 6
$1   #CHROM : 1
$2      POS : 10177
$3       ID : .
$4      REF : A
$5      ALT : AC
$6     QUAL : 100
$7   FILTER : PASS
$8     INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00102;SAS_AF=0
.4949
$9   FORMAT : GT
$10  SAMPLE : 1|0
<<< 6

>>> 7
$1   #CHROM : 1
$2      POS : 10177
$3       ID : .
$4      REF : A
$5      ALT : AC
$6     QUAL : 100
$7   FILTER : PASS
$8     INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00103;SAS_AF=0
.4949
$9   FORMAT : GT
$10  SAMPLE : 1|0
<<< 7

>>> 8
$1   #CHROM : 1
$2      POS : 10177
$3       ID : .
$4      REF : A
$5      ALT : AC
$6     QUAL : 100
$7   FILTER : PASS
$8     INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00105;SAS_AF=0
.4949
$9   FORMAT : GT
$10  SAMPLE : 1|0
<<< 8

>>> 9
$1   #CHROM : 1
$2      POS : 10177
$3       ID : .
$4      REF : A
$5      ALT : AC
$6     QUAL : 100
$7   FILTER : PASS
$8     INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00106;SAS_AF=0
.4949
$9   FORMAT : GT
$10  SAMPLE : 1|0
<<< 9

>>> 10
$1   #CHROM : 1
$2      POS : 10177
$3       ID : .
$4      REF : A
$5      ALT : AC
$6     QUAL : 100
$7   FILTER : PASS
$8     INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00114;SAS_AF=0
.4949
$9   FORMAT : GT
$10  SAMPLE : 0|1
<<< 10

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