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Test-drive the GATK tools and Best Practices pipelines on Terra
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Empty INFO entries for "RankSums"
After running the GATK pipeline, about one third of my variants have no entries for BaseQRankSum, ClippingRankSum, or MQRankSum, which also causes FS=0. This makes hard filtering challenging, because I automatically lose a third of the total SNPs if I try to filter by any of those parameters. I was wondering what causes these empty entries, and if it can be avoided.