Hi, I have simple question: Is it possible to force the QUAL field from a gvcf file to be loaded by vds.combiner? This value would be useful for calculating various fields required by VQSR (at later stages of analysis - after combining gvcf files).
Best regards, PW
It’s not possible at current.
For variants, QUAL and PL[0] are approximately the same value. Could you use LPL[0] for an approximate qual for your purposes?
QUAL
PL[0]
LPL[0]
Are there plans to force the QUAL field in the future?