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Hi @Sheila, Do you konw when the --includeNonVariantSites option will be avalible for GATK4? My colleagues and I are in urgent need of this function.
@Sheila Hi Sheila, Thanks for your reply. 1) They are Phred Scaled scores in BGISEQ data. 2) Did you mean that the PL can be spcified as any one of the valid values, and the PL information will not affect BQSR? Then why does BQSR program check th…