Find SNPs among samples

Question

[asgara]

Hello!

I would like to calculate the number of SNPs in a sample (.vcf file) only located in specific genomic regions (which I have as .bed file). Also, having two samples (as 2 different .vcf files), I would like to do the same as above but reporting only the SNPs which are present in sample 2 and not in sample 1, and still only located in the genomic regions provided as .bed file.

They are small files and I was thinking if that can be solved with some Python code.

Any suggestions?

I hope the description of the problem was understandable and not too confusing.

Thanks!

[Pierre Lindenbaum]

have a look at bcftools view read the manual about --regions-file and --include . http://samtools.github.io/bcftools/bcftools.html

[asgara]

Thanks for the answer! I know there are some existing tools which can probably do it smoothly, but I was wondering if the same results can be obtained also with some Python code.

Answer 1

[tdfyoder]

try VCFtools