Erik Garrison
Just as a point of reference, `vcflib -f` implements techniques to handle filtering the multiallelic cases. A dot is used to specify an allele that has been removed in an...
Sorry, I meant vcflib's `vcffilter -f`. On Dec 19, 2015 10:35 PM, "Erik Garrison" [email protected] wrote: > Just as a point of reference, `vcflib -f` implements techniques to handle >...
I said that I would implement what the group decides--- but I have to admit that it is very low priority to do so given the existence of a straightforward...
@yfarjoun > We are currently implementing allelic-specific filtering as an INFO annotation (AS_FILTER) with count A (one per alternative allele). This is ad-hoc and we would rather use something else...
We will explore applying wfmash to this. It should behave differently in repeats.
Bump.
hey Adam, no, but I was just monkey patching samtools so the .fa.gz reading is thread safe. Would that be helpful?