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Is there a way to limit the genotyping to those sites with FILTER=PASS?
With the genotyping discovery qscript, all the discovery sites were genotyped during the run instead of the much smaller set that have filter=PASS.
Instead of having all these sites genotyped, is there a option to specify that only sites with filter=PASS should be genotyped and output to the final vcf file. Or is there a reason these non PASS sites are included?