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Does HaplotypeCaller detect SNPs which are heterozygous (not matching the refrence allele)?
Dear GATK team,
I have a simple question regarding the HaplotypeCaller/UnifiedGenotype module. There are 3 options for SNPs in the output depended on the reference.
Homozygous for the reference, heterozygous for the reference and alternate nucleotide and homozygous for the alternate nucleotide (0/0, 1/1, 0/1). But what if I would like to have the SNPs which are heterozygous and do not match the reference allel. So e.g. the reference has an A and the mapped reads indicate a G/T. Does one of the module detect that? I have a diploid species and want to get all SNPs. This issue popped up after I had a look on the output of both modules.
Thanks a lot.