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5 votes

PL and QUAL values on VCF file?

The VCF specification provides the definition for the QUAL field. However, QUAL values are often capped by variant callers to a given value. I have seen 100 being used and according to this ...
JRodrigoF's user avatar
  • 827
1 vote

What is the meaning of "Filtering allele frequency" in the gnomAD database?

My understanding is from Whiffin et al. 2017. Imagine a dominant mendelian disease A with complete penetrance, caused only by one allele, which is currently unknown. In your search for that unknown ...
ning's user avatar
  • 141
1 vote

GATK variant filtration using "SelectVariants" and use of JEXL queries

I am following the guidelines given in this links for variant selection for some specific cases that are not as much detailed in the GATK site.
everestial's user avatar

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