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GenotypeGVCFs 3.7 gives different results depending on sharding
Broad's BP joint calling workflow shards GenotypeGVCFs by genomic locations. I was tasked to port the BP workflow from GATK4 to GATK3.7, and reference genome 37.
I was not able to find an equivalent of the hg38.even.handcurated.20k.intervals file for hg37, so tried to make one myself. (I believe people have asked before on this forum for hg38 versions of these intervals, or an explanation of how they were created).
I found that depending where the intervals lie, different calls are emitted by GenotypeGVCFs. The first difference I have seen is that ALT '*' alleles are not called if the upstream deletion is outside the interval.
Called with these shards:
21 10707250 . CTTTGTGA C 140.17 . AC=1;AF=0.0005097;AN=1962;BaseQRankSum=2.25;ClippingRankSum=0;DP=1 21 10707253 rs71227073 T A,* 15301.9 . AC=96,1;AF=0.049,0.0005097;AN=1962;BaseQRankSum=1.62;Clipping... VS 21 10707250 . CTTTGTGA C 140.17 . AC=1;AF=0.0005097;AN=1962;BaseQRankSum=2.25;ClippingRankSum=0;DP=1 21 10707253 rs71227073 T A 15301.9 . AC=96;AF=0.049;AN=1962;BaseQRankSum=1.62;ClippingRankSum=0;DB;D
Is this expected behaviour? IE that calls near the shard boundaries are incorrect?
Is there documentation about the method used to create hg38.even.handcurated.20k.intervals ?
Is there a way to workaround this issue?