filter multiple VCF files using snpSift

Question

[jan]

Hi,

I have several hundreds annonated VCF files (annotated using snpEff). I want to filter out all the low quality and low impact variants in all VCF files. Is there a way to filter all files at one time, rather than filtering each file one by one? I'm planning to use snpSift to filter out the low quality variants.

[Pierre Lindenbaum]

Is there a way to filter all files at one time, rather than filtering each file one by one?

why is the 2nd option a problem?

[jan]

I wasn't clear in my question. I wanted to ask how to automatically search a gene in all of my files without having to manually do the same thing for all files. I could just do a loop.

Answer 1

[h.mon]

Why not do a loop? It is not "all at one time", but it automates the "one by one".

[jan]

Somehow I wasn't thinking about doing a loop. Thank you for the suggestion

[jamesmatthewhamilton]

Why use a loop? The dbsnp is loaded into memory first, and you would end up reloading the dbsnp into memory N times. There has to be a way to load the dbsnp into memory and apply those annotations to N vcf files. Any help with this?