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cumc / xqtl-protocol

Molecular QTL analysis protocol developed by ADSP Functional Genomics Consortium
https://cumc.github.io/xqtl-protocol/
MIT License
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fix the logic for genotype set to missing #899

Closed dianacornejo closed 6 months ago

dianacornejo commented 6 months ago

I have changed the logic to set to missing -S . those genotypes that are not included in that expression. So that if the genotype has DP >= threshold & GQ>= certain threshold it will not be set to missing but if it does not match that expression then It'll be set to missing. This allows for the removal of genotypes that have bad quality by including just the good ones. Notice that we used & instead of && since the criteria needs to be met within the same sample. For reference look at here.

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