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All SNPs are heterozygous

BlueBlue Member

All of my whole-genome sequenced individuals are a cross of different outbred lines with one reference line - effectively identical to the reference genome used for read mapping and variant calling. Thus, effectively all SNPs are heterozygous relative to the reference genome.

Should I alter the settings on the Unified Genotyper to maximise detection of these kind of variants ?

Best Answer


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