GATK Reproducibility #107
yashpatel6
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GATK Reproducibility
#107
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Potential issues with reproducible variant calls with GATK HaplotypeCaller:
With GATK's HaplotypeCaller, there's an issue with reproducing 100% of the variants called when running the caller with the same BAM twice. The discordance is roughly 2-3%.
Publication identifying reproducibility issue with GATK's HaplotypeCaller: https://academic.oup.com/bioinformatics/article/32/15/2243/1743552
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