Entering edit mode
5.3 years ago
reza
▴
300
i performed variant calling in mitochondria using whole genome sequencing data by GATK UnifiedGenotyper. Genotype of some SNPs specially those are in D-loop region is heterozygote (0/1). Is it due to heteroplasmy?
possibly. you can set --ploidy in GATK to 100 if you want to drop the assumption of diploid genomes
when i set -ploidy 100, numbers of identified SNPs increased from 23 to 593 ! without apply of -ploidy on 100, my results (23 SNPs) are correct?