Can you please provide
a) GATK version used ：188.8.131.52
b) Exact GATK commands used
c) The entire error log if applicable.
First， I am wondering if the data is whole genome sequencing，is it necessary to add DP < min || DP > 2.5 times avrage depth in Hard-filter step? I konw that QualByDepth has already consider the depth value，
Second，RemoveNearbyIndels,"This is a preprocessing step for the CRSP sensitivity validation truth data. " what's the CRSP?Clinical Research Sequencing Platform (CRSP)? or ....?
and after HaplotypeCaller step, GATK team don't recommend removing SNPs that are close to indels systematically, while is it necessary to RemoveNearbyIndels
The last one,some papers wrote methods mutation must be supported by at least 2/5 reads each direction,and I am wondering how to filter this criteria？Use IGV manually to filter？
Look forward to your favourable reply.
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