Question: filter multiple VCF files using snpSift
0
gravatar for jan
5.0 years ago by
jan130
Sydney, Australia
jan130 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 • 1.7k views
ADD COMMENTlink modified 3.7 years ago by Biostar ♦♦ 20 • written 5.0 years ago by jan130

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 REPLYlink modified 11 months ago by RamRS30k • written 5.0 years ago by Pierre Lindenbaum131k

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 REPLYlink modified 11 months ago by RamRS30k • written 5.0 years ago by jan130
1
gravatar for h.mon
5.0 years ago by
h.mon31k
Brazil
h.mon31k wrote:

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

ADD COMMENTlink modified 11 months ago by RamRS30k • written 5.0 years ago by h.mon31k

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

ADD REPLYlink written 5.0 years ago by jan130
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