Giraffe DeepVariant workflow

Question

[DBScan]

Hi, I am currently playing around with pangenome approaches using vg giraffe and DeepVariant. I was that there is an official workflow here https://github.com/vgteam/vg_wdl?tab=readme-ov-file#giraffe-deepvariant-workflow. I'm not very fluent in reading WDL scripts, but it looks like there is for instance no adapter trimming involved? I've read some papers and there was also no mention of adapter trimming. So basically the only steps are:

1. Running vg giraffe
   1. Sorting the resulting bam
   2. Calling variants with DeepVariant

Is this correct?

Answer 1

[Istvan Albert]

for modern mappers trimming is not needed because they can and will softclip overhangs

a typical variant calling is indeed just: alignment -> call

[DBScan]

Thanks, that is what I expected!