How to efficiently count missense mutations from an annotated vcf file?

Question

[Bienvenido IV A. David]

Hi! I am currently working on my undergraduate study about the frequency of missense mutations in early and advanced stages of early luminal breast cancer. The vcf file contains 47 transcriptomic samples--12 early (stage II) and 35 advanced (III)--and were annotated using SnpEff eff on Galaxy. Is there a tool I can use to efficiently count the mutations by sample and by position per chromosome? I would also appreciate any suggestions for downstream or enrichment analysis for my study.

EDIT: I am more than willing to walk you through the RNA-Seq pipeline I am using on Galaxy. Any assistance or suggestions are much appreciated, as I am admittedly new to bioinformatics.

Answer 1

[Pierre Lindenbaum]

. Is there a tool I can use to efficiently count the mutations by sample and by position per chromosome?

bcftools stats

but your title says "How to efficiently count missense mutations from an annotated vcf file?". So per sample , that it be something like:

bcftools query -l in.vcf | while read S; do echo -s "${S}: " && bcftools view -Ou  --trim-alt-alleles --samples "${S}" in.vcf |bcftools view -c1 | grep -F 'missense' | wc -l ; done