Does GATK work with polypolids?
Hi, I would like to use GATK for SNP variant and indel variant calling in wild relatives of a crop plant. I have a good reference genome for the diploid crop where I could map my reads but my species where I would like to call the SNPs are di- tetra and hexaploid. I wanna trace there ancestry. Can I use GATK as a platform to call the genome wide SNPs?