Question: How to preprocess, normalize, decompose a VCF file before inputting to the SNPEff?
0
gravatar for human_genomeXXX
3.4 years ago by
human_genomeXXX10 wrote:

How to preprocess, normalize, decompose a VCF file before inputting to the SNPEff? Heard, people use -sed and -grep to process VCFs somehow.

snpeff vcf • 1.4k views
ADD COMMENTlink written 3.4 years ago by human_genomeXXX10

Yes you can use sed and grep. For a more detailed answer, please add some context to your question.

ADD REPLYlink written 3.4 years ago by RamRS27k

There is a "cant find chromosome error" in SNPEff output see VCF`s headers C: How to reduce annotation errors using SNPEff on BBMap`s and Pilon`s VCFs?. What exactly commands can fix that? thank you

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by human_genomeXXX10

I don't get the point about what you are exactly looking for, but bcftools is always a nice option for VCF processing.

ADD REPLYlink written 3.4 years ago by iraun3.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 993 users visited in the last hour