So I joint called 3 cohorts: Cases-A, Cases-B, Control. Cases-A and Control used 2 different platforms but the same one across samples within each cohort.
It was recently brought to my attention that Cases-B was sequenced on 2 different platforms; however, when I genotyped them, I just used a single interval file.
Does this have an impact on my joint calling? I thought this should (?) not impact anything. My line of thinking is that, because all the cohorts are being joint called, one could theoretically only use 1 interval file across all the cohorts since joint calling will only look at the intersecting intervals anyways. Then, finally, if one platform or another does not sequence in a particular place defined by the single interval file, there would be differential missingness in that area and those genomic intervals to be removed by QC.
Is this true or I should definitely make sure to re-genotype and joint call the data? What is the reason to do this?
