Homopolymer filter for nanopore data

[iqbal-lab]

Looks like right place to do this is in varifier, at the point when have an MSA, before making the VCF.
Have pre-specified threshold for number of bases in a homopolymer in the ref genome, and at any position where there
is a longer homopolymer than that threshold, basically refuse to call an indel - revert back to the reference.
Lots of fun edge cases with dropped amplicons overlapping homopolymers etc.

(Assumption: no primer has a homopolymer in it...)

[iqbal-lab]

This is done