Beginner to Exome Seq
Just beginning to work with exome sequence and I have a basic question. In my excel file there is a column labeled "gnomad filter." Within the column are the following notations: PASS, RF, AC0, INBREEDING COEFF, or blank. Trying to eliminate those results that are the result of poor qc. If these are listed, does that mean they passed or failed? What is the significance of each? Is better or worse than the others? My first run, I looked at only "PASS" but was so restrictive that it eliminated a mutation that we knew was there.
Thanks, Debbie
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You should be looking at the VCF file and not a tabular file on Excel. Aside from the fact that Excel can mess up data, all the metadata you're looking for is in the VCF file. You describe something called "gnomad filter", but the content looks more like the FILTER column of a VCF, each value of which (PASS, RF, AC0, etc.) will be defined and described in the VCF header.
https://twitter.com/dgmacarthur/status/261310059554930688
FAILED
it is declared in the VCF header of the gnomad VCF file.