Adding a test to capture an expected edge case in Reblocking #8928
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ldgauthier
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Jul 29, 2024
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Running the scientific tests in WARP when updating GATK from 4.5.0.0 -> 4.6.0.0 caught a difference in ReblockGVCFs when a no call site with GQ=0 was derived from a low quality call where the PLs with a value of 0 were in an allele that was subset (e.g.
<NON_REF>). I believe this new behavior is a feature because it now correctly outputs a ref block with GQ=0.This test provides an example of one of these cases to ensure that the behavior stays the same in the future.