jvarkit

VcfCompareCallersOneSample

For my colleague Julien: VCF with one sample called using different callers. Only keep variant if it was found in min<x=other-files<=max

Usage

Usage: vcfcomparecallersonesample [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit
    -M
       max number of challengers found, inclusive.
      Default: 2147483646
    -a
      ignore ALT allele
      Default: false
    -f
      VCF to be challenged.  Must be sorted on dict. Must contain a dict.
      Default: []
    -m
      min number of challengers found, inclusive.
      Default: 0

Keywords

• vcf
• compare

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 vcfcomparecallersonesample

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/vcfcmp/VcfCompareCallersOneSample.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 vcfcomparecallersonesample ? 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

Misc.

I used

java -jar dist/VcfCompareCallersOneSample.jar  -m1 -M1 -f samtools.vcf gatk.vcf
java -jar dist/VcfCompareCallersOneSample.jar  -m1 -M1 -f gatk.vcf samtools.vcf

shouldn’t I get the same number of variants in both files ? Answer is “not always” in the following case:

in gatk.vcf:

11	244197	rs1128322	T	C

in samtools.vcf:

11	244197	rs1128322	T	C,G

in

java -jar dist/VcfCompareCallersOneSample.jar  -m1 -M1 -f samtools.vcf gatk.vcf

we keep the variant because we found ‘C’ in samtools and ‘gatk’

java -jar dist/VcfCompareCallersOneSample.jar  -m1 -M1 -f gatk.vcf samtools.vcf

the variant is discarded because ‘G’ is found in samtools but not in ‘gatk.vcf’

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