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--stand_emit_conf and --stand_call_conf setting in Haplotypecaller
I have processed samples using GATK 3.1 Haplotypecaller according to the RNA Seq best practice.
Haplotypecaller is set with --stand_emit_conf = 20 and --stand_call_conf = 20 options, but I could find variants which QUAL less than 20 in the output gVcf file and variants which its QUAL < 20 is not marked as LowQual.
I wonder what those parameters do for Haplotypecaller.
I have run with --stand_emit_conf = 20 and --stand_call_conf = 30 for testing. Output gvcf file appears to be identical.