Questions tagged [variant-filtration]

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3 votes
1 answer
242 views

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

Recent gnomAD versions include a "filtering allele frequency" which tells you when a variant can be safely adjudged not to be disease-causing. Unfortunately, I'm having trouble making sense ...
3 votes
1 answer
297 views

PL and QUAL values on VCF file?

I want to filter my VCF file to include only the relevant information I need but I have some questions about the results I got. This is what the first 10 lines of my VCF file looks like: ...
2 votes
0 answers
88 views

Difference between pileup and mpileup in VarScan and samtools

I'm going to call variants with VarScan from a pileup files created with samtools. I realized that there are in general two major possibilities to call variants, pileup as well as mpileup. The VarScan ...
1 vote
1 answer
553 views

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

How to do variants selection in some corner cases using GATK and JEXL expressions? I am following the guidelines given in this links for variant selection for some specific cases are not as much ...