search

DecodeGenetics / graphtyper

Population-scale genotyping using pangenome graphs
http://dx.doi.org/10.1038/ng.3964
MIT License
167 stars 20 forks source link

support for haploid/different ploidy #16

Open alexweisberg opened 5 years ago

alexweisberg commented 5 years ago

Hi,

I am really interested in using graphtyper for my bacterial genome SNP calling as there is a lot of diversity in some lineages and typical SNP calling pipelines run into issues when strains are fairly diverged from a reference. I was able to run graphtyper on a bacterial genome dataset, and manual inspection of the output shows several heterozygous variant calls (0/1) which are incorrect with a haploid genome. I was wondering if there is an option to set the ploidy level for SNP calls? Thanks!

Best, Alex

hannespetur commented 5 years ago

Hello, thanks for posting. It is currently not possible to set the ploidy level but we will likely add the option of haploid in the future. For now, I would suggest filtering the heterozygous sites.

All the best, Hannes