jvarkit

VcfNoCallToHomRef

Last commit

Convert the UNCALLED gentoypes in a VCF to HOM_REF. This tool can be used after using GATK CombineVariants.

DEPRECATED

use bcftools plugin: +setGT

Usage

Usage: vcfnocall2homref [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
    -dp, --depth
      Default DEPTH. negative = don't set depth.
      Default: 10
    -f, --filter
      Set this **Genotype** FILTER for converted genotype
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -gq, --gq, --GQ
      Default Genotype quality: negative : don't set GQ.
      Default: 1
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -s, --includeSamples
      only converts those samples. Default: all samples are converted.
      Default: []
    -sf, --includeSamplesFile
      only converts those samples. Default: all samples are converted. One 
      sample per line.
    -o, --out
      Output file. Optional . Default: stdout
    -p, --ploidy
      ploidy
      Default: 2
    --version
      print version and exit

Keywords

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 vcfnocall2homref

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

Creation Date

20170914

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/VcfNoCallToHomRef.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 vcfnocall2homref ? 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

deprecated. Use bcftools +setGT

Example

original VCF

##fileformat=VCFv4.2
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##contig=<ID=rotavirus,length=1074>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2	S3	S4
rotavirus	51	.	A	G	22.55	.	.	GT:PL	./.	0/0:0,255,127	0/0:0,255,137	1/1:70,255,0
rotavirus	91	.	A	T	5.45	.	.	GT:PL	0/0:0,255,133	0/1:40,0,31	./.	./.

default invocation

$ java -jar dist/vcfnocall2homref.jar input.vcf
##fileformat=VCFv4.2
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##contig=<ID=rotavirus,length=1074>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2	S3	S4
rotavirus	51	.	A	G	22.55	.	AC=2;AF=0.25;AN=8;DP=10	GT:DP:GQ:PL	0/0:10:1	0/0:.:.:0,255,127	0/0:.:.:0,255,137	1/1:.:.:70,255,0
rotavirus	91	.	A	T	5.45	.	AC=1;AF=0.125;AN=8;DP=20	GT:DP:GQ:PL	0/0:.:.:0,255,133	0/1:.:.:40,0,310/0:10:1	0/0:10:1

convert S3 and S4 only

$ java -jar dist/vcfnocall2homref.jar  -f CONVERTED -s S3 -s S4  ~/jeter.vcf 
##fileformat=VCFv4.2
##FILTER=<ID=CONVERTED,Description="NOCALL Genotypes converted to HOM_REF by com.github.lindenb.jvarkit.tools.misc.VcfNoCallToHomRef">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=FT,Number=.,Type=String,Description="Genotype-level filter">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##contig=<ID=rotavirus,length=1074>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2	S3	S4
rotavirus	51	.	A	G	22.55	.	AC=2;AF=0.33333334;AN=6;DP=0	GT:PL	./.	0/0:0,255,127	0/0:0,255,137	1/1:70,255,0
rotavirus	91	.	A	T	5.45	.	AC=1;AF=0.125;AN=8;DP=20	GT:DP:FT:GQ:PL	0/0:.:PASS:.:0,255,133	0/1:.:PASS:.:40,0,31	0/0:10:CONVERTED:1	0/0:10:CONVERTED:1

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