jvarkit

VcfCutSamples

Select/Exclude some samples from a VCF

DEPRECATED

use bcftools or gatk SelectVariants

Usage

Usage: vcfcutsamples [options] Files
  Options:
    --disable-vc-attribute-recalc
      When genotypes are removed/changed, Dd not recalculate variant 
      attributes like DP, AF, AC, AN...
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --invert
       invert selection
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
    --outputbcf
      Output bcf (for streams)
      Default: false
    -f, --samplefile
      read file containing sample names
    -S, --samples
      Sample name
      Default: []
    --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
    --vcfcreateindex
      VCF, create tribble or tabix Index when writing a VCF/BCF to a file.
      Default: false
    --vcfmd5
      VCF, create MD5 checksum when writing a VCF/BCF to a file.
      Default: false
    --version
      print version and exit
    -E
       a missing sample is an error
      Default: true
    -r
      remove variant if no call at all
      Default: false

Keywords

• vcf
• sample

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcfcutsamples

The java jar file will be installed in the dist directory.

Source code

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

Unit Tests

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

$ curl  "https://raw.github.com/arq5x/gemini/master/test/test5.vep.snpeff.vcf" |\
  java -jar dist/vcfcutsamples.jar  -S M10475 -S M128215 |\
   grep "CHROM" -A 2

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	M128215	M10475
chr1	145273345	.	T	C	289.85	.	AC=3;AF=0.38;AN=8;BaseQRankSum=1.062;CSQ=missense_variant|Tct/Cct|S/P|ENSG00000213240|NOTCH2NL|ENST00000369340|4/6|benign(0.238)|tolerated(0.45),missense_variant|Tct/Cct|S/P|ENSG00000213240|NOTCH2NL|ENST00000362074|3/5|benign(0.238)|tolerated(0.45),missense_variant&NMD_transcript_variant|Tct/Cct|S/P|ENSG00000255168||ENST00000468030|3/23|benign(0.416)|tolerated(0.55),missense_variant|Tct/Cct|S/P|ENSG00000213240|NOTCH2NL|ENST00000344859|3/6|possibly_damaging(0.545)|tolerated(0.44);DP=1000;DS;Dels=0.00;EFF=EXON(MODIFIER|||||RP11-458D21.5|nonsense_mediated_decay|NON_CODING|ENST00000468030|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S67P|230|NOTCH2NL|protein_coding|CODING|ENST00000344859|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S67P|236|NOTCH2NL|protein_coding|CODING|ENST00000362074|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S67P|236|NOTCH2NL|protein_coding|CODING|ENST00000369340|);FS=3.974;HRun=1;HaplotypeScore=17.4275;MQ=29.25;MQ0=0;MQRankSum=-1.370;QD=0.39;ReadPosRankSum=-1.117	GT:AD:DP:GQ:PL	0/1:215,34:250:99:269,0,3796	0/0:226,22:250:99:0,158,4259
chr1	156011444	.	T	C	2523.46	.	AC=4;AF=0.50;AN=8;BaseQRankSum=-0.490;CSQ=missense_variant|atA/atG|I/M|ENSG00000160803|UBQLN4|ENST00000368309|10/11|benign(0.012)|tolerated(0.3),downstream_gene_variant|||ENSG00000160803|UBQLN4|ENST00000459954|||,missense_variant|Atc/Gtc|I/V|ENSG00000160803|UBQLN4|ENST00000368307|6/7|unknown(0)|tolerated(0.88);DP=204;Dels=0.00;EFF=DOWNSTREAM(MODIFIER|||||UBQLN4|processed_transcript|CODING|ENST00000459954|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I148V|226|UBQLN4|protein_coding|CODING|ENST00000368307|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I495M|601|UBQLN4|protein_coding|CODING|ENST00000368309|);FS=4.328;HRun=0;HaplotypeScore=4.3777;MQ=35.24;MQ0=0;MQRankSum=-0.101;QD=14.93;ReadPosRankSum=1.575	GT:AD:DP:GQ:PL	0/0:34,1:35:69:0,69,717	0/1:24,15:40:99:214,0,443

##See also

• [[AlleleFrequencyCalculator]]
• http://vcftools.sourceforge.net/htslib.html#subset

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