Does the pipeline use the first allele or the second allele as reference when reading the .pgen files? #156
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smlmbrt
scienception
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Is there a flag to specify this or does the software figures it out automatically? |
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Answered by
smlmbrt
Aug 24, 2023
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The pipeline doesn't use REF/ALT annotations per se, as it can calculate the PGS regardless of whether the effect_allele is the REF or ALT as we allow for both when matching the PGS variants to the genotyping data. In the plink format the 3'rd column of the .pvar file is the REF (https://www.cog-genomics.org/plink/2.0/formats#pvar), similar to VCF. |
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The pipeline doesn't use REF/ALT annotations per se, as it can calculate the PGS regardless of whether the effect_allele is the REF or ALT as we allow for both when matching the PGS variants to the genotyping data. In the plink format the 3'rd column of the .pvar file is the REF (https://www.cog-genomics.org/plink/2.0/formats#pvar), similar to VCF.