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Did the UnifiedGenotyper of previous builds use to place "PASS" in the filter fields of vcf files? I have re-ran some data using current best practices, including the HaplotypeCaller. My first snps.indels.raw.vcf file has all . in the FILTER field, which I remember was not a good thing. Im compared the vcf produced at this step with my previous UnifiedGenotyper counterpart and the FILTER field was populated with "PASS". I am bit concerned that is there were no PASS then no LowQual filter applied by the caller either.
Besides using HaplotypeCaller, the only other argument I had changed was returning the -stand_emit_conf to the default. Is this perhaps the root of my concern? Does having both stand_call_conf and stand_emit_conf at defaults ie. equal not apply any FILTER?