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atks / vt

A tool set for short variant discovery in genetic sequence data.
http://genome.sph.umich.edu/wiki/vt
MIT License
192 stars 3 forks source link

Consecutive SNPs #98

Closed nurmians closed 5 years ago

nurmians commented 5 years ago

At least GATK4/Mutect2 calls two consecutive SNPs as:

CHROM COORD ID REF ALT
chr2 110666292 . AC GT

would be nice if vt normalize was able to split it into:

CHROM COORD ID REF ALT
chr2 110666292 . A G
chr2 110666293 . C T

I had to do this with another script after normalization to be able to compare the calls.

atks commented 5 years ago

you can use the command blocksub