To extract uniques SNPs froma. multisample VCF file

Question

[sam]

Hi,

I have a multi-sample VCF file. This VCF contains around 20 samples (Sample1 - Sample20).

I intend to extract unique SNPs of Sample1 compared to all the other samples ()samples2 - samepls20).

Samtools has a contrast plugin to extract genotypes that are not observed in another. Here I want to compare my sample of interest against the rest.

Is there any best way I could achieve the unique SNPs? Or should I split my multi-sample VCF file into individual VCF files and do the comparison?

Thank you!

Answer 1

[Pierre Lindenbaum]

using vcffilterjdk: https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/

java -jar jvarkit.jar vcffilterjdk -e 'final String sn1="sampleName"; final Genotype g1=variant.getGenotype(sn1); return variant.getGenotypes().stream().filter(G->!G.getSampleName().equals(sn1)).allMatch(G->!G.sameGenotype(g1));' input.vcf.gz

[sam]

Thanks Pierre! I shall try this solution.

[sam]

Hi Pierre,

I tried to install the software and i get the following error:

* What went wrong:
  Execution failed for jvarkit com.github.lindenb.jvarkit.tools.jvarkit.JvarkitCentral.
  > Compile failed; see the compiler error output for details

Sorry, I am not good at java. I guessed you would already know the solution for this error. So posting here again.

I could write a python script but would like to know if there is a package that could do this already.

Thank you!