Find SNPs among samples
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2.9 years ago
asgara • 0

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!

SNP gene genome python • 487 views
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have a look at bcftools view read the manual about --regions-file and --include . http://samtools.github.io/bcftools/bcftools.html

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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.

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2.9 years ago
tdfyoder ▴ 40

try VCFtools