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Unified genotyper with target region vs without target region
I am running some exome samples with UG. I tried this in 2 ways:
1. Run UG and then apply exome region filter.
2. Run UG with exome regions.
Is there any difference in these approaches if I am only concerned about the variants in exome region?
I have ran in both ways and on comparison I see that some values are different for the same locus. For eg. PL, MQRankSum, BaseQRankSum. However, the different is not huge but does UG perform slightly differently for making calls with target regions vs without?
PS: I have ran this for UG with multiple samples