variant calling in mitochondria using whole genome sequencing

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?

mitochondria snp

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written 7.6 years ago by reza

possibly. you can set --ploidy in GATK to 100 if you want to drop the assumption of diploid genomes

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written 7.6 years ago by Jeremy Leipzig

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?

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written 7.6 years ago by reza

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