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CollectSequencingArtifactMetrics PreAdapterDetailMetrics question
Dear GATK support,
I'm trying to figure out how the error_rate and qscore is calculated in the Picard sequencing artifact metrics. I notice that in the PreAdapterDetailMetrics, for two reverse compliment context, the pro and con ref bases and alt bases are exact opposite, which lead to one to be scored 100 and the other in the 30s. And I got confused now are the pro_ref_bases and con_ref_bases generated? Shouldn't they be the same because they are just reverse comp copy of each other? Example shown below.
REF_BASE ALT_BASE CONTEXT PRO_REF_BASES PRO_ALT_BASES CON_REF_BASES CON_ALT_BASES ERROR_RATE QSCORE
C T TCT 33803861 34212 33838997 62648 0 100
G A AGA 33838997 62648 33803861 34212 0.00042 34
Another related question is, is there any guideline that we can use as recommended cutoff score to define whether a certain base change is artifact instead of true variant?