--recall that turns off augmentation and changes up a bunch of calling options to be better on SVs
--genotype_vcf which does the same as --recall but works on a given VCF
This has already lead to some confusion in the SV paper, as --recall does so much more than its name implies. What we need is
single option to turn augmentation on and off (maybe can keep --recall for this
and a bunch of good defaults that will do a good job on snps and SVs with minimum fiddling by the user.
There is a bit of a challenge with this as turning off augmentation does necessitate using average support etc., but the status quo can certainly be at least improved.
Right now we have
--recallthat turns off augmentation and changes up a bunch of calling options to be better on SVs--genotype_vcfwhich does the same as--recallbut works on a given VCFThis has already lead to some confusion in the SV paper, as
--recalldoes so much more than its name implies. What we need is--recallfor thisThere is a bit of a challenge with this as turning off augmentation does necessitate using average support etc., but the status quo can certainly be at least improved.