How does one execute this script?
• 1 views
•
link
written
by
deepti1rao •
Is there a way to reformat vcf 4.2 down to 4.1?
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.
• 7,249 views
•
link
updated
by
biostars •
•
written
by
umn_bist •
•
written
by
umn_bist •
1 answer
Try this script (courtesy of Daniel Cook).
• 1 views
•
link
written
by
harold.smith.tarheel
Put it into your .bashrc, source that file again (source ~/.bashrc) and execute as vcf_downgrade oldfile.vcf
• 0 views
•
link
written
by
biostars •
Log in to answer this question.
More posts like this
-
Annotate WGS VCF with Allele Frequencies
written by Gabriel •
-
Determine strand info of somatic mutations
written by whb •
-
stats file in Mutect2 calling
written by dentepre •
-
Annotating varscan2 output
written by ar.satkhol18 •
-
Problem with .vcf annovar
written by zizigolu
-
Filtering Mutect2 calls post annotation with SnpEff
written by philomath_physicus •
-
Tools to filter Mutect2 output
written by nanana
-
Any experience using SomaticSeq for RNAseq SNV?
written by umn_bist •
-
MuTect2 - vcf 4.1 instead of vcf 4.2
written by umn_bist •
-
[mutect2] vcf 4.1 instead of vcf 4.2?
written by umn_bist •
