incorporating angsd into SNPArcher

[linnea-schaefer]

Hi there,

I have a dataset of ~110 samples of variable coverage, some of which are too low for hard-genotyping. Is there a way to incorporate angsd into the SNPArcher workflow? I see an environment for it but couldn't find any documentation on how to use it.

Thanks so much,
Linnea

[tsackton]

snpArcher does not support any native way to run ANGSD. In principle, you can use GATK to output a VCF with genotype likelihoods, and then import that into ANGSD, but I don't know how reliable ANGSD's ability to read genotype likelihoods from VCFs is.