Print Minimum Depth from a VCF

Question

[QVINTVS_FABIVS_MAXIMVS]

Is there an easy way to print the minimum depth (FORMAT:DP) for variants in a VCF.

I can write a script to accomplish this, but I am looking for an option in bcftools or some other tool that can determine the minimum depth on the fly.

Answer 1

[Pierre Lindenbaum]

using bioalcidaejdk http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html

$ java -jar dist/bioalcidaejdk.jar -e 'stream().forEach(V->{println(V.getContig()+":"+V.getStart()+":"+V.getReference().getDisplayString()+"\t"+V.getGenotypes().stream().filter(G->G.hasDP()).mapToInt(G->G.getDP()).min().orElse(-1));});' input.vcf