Not able to handle missing sites

[Hjorvik]

Hi!

I'm trying to use graphtyper to call genotypes on a bunch of sheep genomes, but the output is just the header of the VCF file with no variant called. When I check the logs, every few positions I get the message
" constructor.cpp:1495 Ignoring alt. allele NATTG at pos=21915. Non-ACGT base."

Is graphtyper not able to deal with Ns? How should I deal with those sites/reads then?

[hannespetur]

No sorry