Viltering VCF file with Exonic variants via Python

Question

[a_biologist]

Hello All,

I have a VCF file and I want to filter the file with exonic variants only and through out the intronic ones. I have done it using a python script but it still not doing it so and the run takes a long time to do so. Is there a faster way to do this?

Thanks

[Sam]

So you are just trying to identify exonic variants? Try using Annovar or KGGSeq

[a_biologist]

Hi Sam, I could do that but instead I want to filter out only variants that are with an exonic region I don't want them annotated for the time being just get a new resulted vcf file that is filtered with exonic variants and that's why I used python to do so.

Thanks

[Sam]

Well, once you have them annotated, you can just get the coordinates of those snps that you want and use any programme you like to filter them from the vcf file. It will be much faster and simpler, no point in reinventing the wheel unless you are trying to develop a new programme

Answer 1

[Devon Ryan]

Just use bedtools intersect and provide it with your VCF file and a BED file containing the exons (I'm not entirely sure this would work with a GFF file, since it might then give you anything overlapping a gene).

Answer 2

[fashiondesignrussian]

Try VCFMiner from Mayo, latest releases of DNAstar software suite have also some tools to play with VCFs, try R packages, perhaps