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quang

Hi all, I have a question about HaplotypeScore in GATK. In the 1000GP paper, Broad uses 8 metrics (including HaplotypeScore) to estimate the final quality scores for variants. However, GATK does not produce HaplotypeScores for all variants for my sequencing data (600 samples, 10x coverage). So I would like to ask a question: Did Broad meet the same problems with 1000GP data and how did you handle that? What HaplotypeScore value should we assign for the variants or we just leave the variants out? thanks very much, best regards, Quang.

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