filter multiple VCF files using snpSift
1
0
Entering edit mode
5.7 years ago
jan ▴ 150

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.. 

snpSift filter vcf • 1.9k views
ADD COMMENT
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode
5.7 years ago
h.mon 32k

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1267 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6