Is there a way to reformat vcf 4.2 down to 4.1?

Question

[umn_bist]

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.

Answer 1

[harold.smith.tarheel]

Try this script (courtesy of Daniel Cook).

[deepti1rao]

How does one execute this script?

[biostars]

Put it into your .bashrc, source that file again (source ~/.bashrc) and execute as vcf_downgrade oldfile.vcf