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mae - .vcf filtering #397

Answered by vyepez88
bpuzek asked this question in Q&A
Nov 23, 2022 · 1 comments · 1 reply
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Hi Barbara,
Thanks for using DROP and your enquiry.
The MAE module is composed of 2 parts, the test for MAE and the sampleQC.
The sampleQC modules uses the 1kg variant file to detect overlapping variants in a sample's DNA and RNA.

Regarding, the test for MAE, a results table is exported per sample containing all tested SNVs located under {root_dir}/processed_results/mae/samples/{vcf}--{rna}_res.Rds. If addAF: TRUE, columns containing the gnomAD maxAF are included, as well as another column called rare which is TRUE/FALSE depending on the maxAF cutoff provided.

We further export tables containing the MAE results of all samples together. Here, results are filtered as well by significance an…

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@bpuzek
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