search

tseemann / snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment
GNU General Public License v2.0
467 stars 113 forks source link

INDELs and depth mask on same consensus sequence #335

Open donutbrew opened 4 years ago

donutbrew commented 4 years ago

Hi there! It would be great to merge the information encoded in the snps.consensus.fa and snps.aligned.fa file, such that both indels and low coverage regions are visible on a consensus sequence. I'm not sure I see an obvious way of merging them after they are generated, but what are your thoughts on revisiting the consensus generation step?

tseemann commented 4 years ago

I had actually forgotten I generate a consensus.fa file; i have never used it.

The .vcf + .aligned.fa is a bit of a hack. It originates to before .gvcf, and it was a way to avoid gigantic VCF files with a line for every site.

You could probably do it manually using the .aligned.fa as a mask to apply to the ref.fa, then apply the .vcf to edit that maybe?

I'll leave this open as an enhancement.