Added sawfish. #175
Added sawfish. #175
Conversation
williamrowell
force-pushed
the
feature/sawfish
branch
from
ff3f24f to
17b2ef6
Compare
williamrowell
force-pushed
the
feature/sawfish
branch
from
17b2ef6 to
011a23f
Compare
There was a problem hiding this comment.
Looks good in general. I'd consider not using the sex-specific ploidy tracks by default for now based on my experience with downstream tools. Probably I should change the behavior to process these regions as haploid internally, but then still output GT values of "0/0" and "1/1" to improve downstream tool compatibiltiy.
| ref_index = ref_map["fasta_index"], # !FileCoercion | ||
| out_prefix = "~{sample_id}.~{ref_map['name']}", | ||
| expected_male_bed = ref_map["hificnv_expected_bed_male"], # !FileCoercion | ||
| expected_female_bed = ref_map["hificnv_expected_bed_female"], # !FileCoercion |
There was a problem hiding this comment.
I'm still a bit on the fence about using the XX and XY ploidy tracks for sawfish in deployment (at least as implemented today). The "0" and "1" GT values on the sex chromosomes seem to be unexpected by a number of downstream pipelines, so this introduces some downstream risk with a pretty minor benefit.
There was a problem hiding this comment.
How does HiPhase handle haploid genotypes? @holtjma
There was a problem hiding this comment.
It will pass them through, we already do this for TRGT
There was a problem hiding this comment.
I was not thinking so much of pb pipeline tools, moreso things like truvari and various sv script bricabrac in use downstream. It's fine for now, but once some kind of CNV integration comes into play then this ploidy file will be essential, so I might make the switch to keep genotypes as 'diploid-formatted-haploid' (ie. 0/0 and 1/1) at that point.
There was a problem hiding this comment.
For now, do you suggest dropping the ploidy support?
There was a problem hiding this comment.
Yes, I think doing so would create fewer downstream problems.
Added sawfish v0.12.7.
sawfish_discoverandsawfish_calltasks.sawfish_calloptionally outputs supporting reads json (defaulttrue) for SVTopoTo do: