SNP filtering for haploid genomes

mikawin

Hello,

Does the GATK team have any recommendations for filtering SNP data for haploid genomes? Our team works with microbial eukaryotes, both haploid and diploid and we have used the GATK v3 best practices for filtering for the latter. [VQSR was not possible, since we do not have access to a truth/high confidence SNP set.]

Thanks, Mika

Geraldine_VdAuwera

Hi Mika,

See this thread for a relevant discussion. Unfortunately as you'll read there we don't have much experience with non-diploid organisms, and little insight to offer. However you may be able to get some advice from the user community by posting this in the "Ask the community" section of the forum.

Good luck!