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 ...
- 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 ...
- 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.
https://gatk.broadinstitute.org/hc/en-us/articles/...
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