Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: filter multiple VCF files using snpSift
0
gravatar for jan
5.3 years ago by
jan • 140
Sydney, Australia
jan • 140 wrote:

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.. 
vcf filter snpsift • 1.8k views
ADD COMMENT • link •
modified 3.9 years ago by Biostar ♦♦ 20 • written 5.3 years ago by jan • 140

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 • link modified 14 months ago by _r_am ♦ 32k • written 5.3 years ago by Pierre Lindenbaum ♦ 133k

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 • link modified 14 months ago by _r_am ♦ 32k • written 5.3 years ago by jan • 140
1
gravatar for h.mon
5.3 years ago by
h.mon ♦ 32k
Brazil
h.mon ♦ 32k wrote:

Why not do a loop? It is not "all at one time", but it automates the "one by one".
ADD COMMENT • link modified 14 months ago by _r_am ♦ 32k • written 5.3 years ago by h.mon ♦ 32k

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

ADD REPLY • link written 5.3 years ago by jan • 140
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1019 users visited in the last hour
_