Question: Is there a way to reformat vcf 4.2 down to 4.1?
0
gravatar for umn_bist
3.5 years ago by
umn_bist330
umn_bist330 wrote:

I've been using MuTect2 (part of GATK toolkit) to call somatic variants for my RNAseq data set. The vcf file is in 4.2 format which I'm not familiar with. Is there any advantage to using 4.2 instead if I'm annotating with snpEff/annovar and filtering with snpSift?

The documentations for annotation/filtering tools have been based on 4.1 vcf format which has proven difficult to follow for my particular vcf files.

Any help will be greatly appreciated.

snpeff snpsift variant calling • 3.5k views
ADD COMMENTlink modified 3.5 years ago by harold.smith.tarheel4.4k • written 3.5 years ago by umn_bist330
0
gravatar for harold.smith.tarheel
3.5 years ago by
United States
harold.smith.tarheel4.4k wrote:

Try this script (courtesy of Daniel Cook).

ADD COMMENTlink written 3.5 years ago by harold.smith.tarheel4.4k

How does one execute this script?

ADD REPLYlink written 16 months ago by deepti1rao20
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