I was trying to use
sample_qc function to compute QC some metrics. The ‘PL’ field of my vcf are all missing, but the ‘GQ’ field are not missing. The error message is:
HailException: PL cannot have missing elements.
My understanding is that the
gq_stats from the
sample_qc function are computed from ‘GQ’ field. But why Hail complains missing elements in PL field? How am I able to compute
gq_stats when my vcf only contains ‘GQ’ but not ‘PL’?