Comments (1)
Hi Elizabeth - I had the same question!
Reading a bit more about the Strelka2 methods (see Supp. Note 2 of their paper) seems like it has two hard-coded
built-in quality filters LowEVS and LowDepth. So if the variant does not meet the thresholds it is marked as LowEVS, LowDepth or both. You can read more about how the EVS is calculated in their methods/supplementary note 2, but basically if the score is lower than the threshold it does not pass QC standards (the thresholds are 6 and 7 for indels and SNVs, respectively: #79). So I would keep only variants marked as PASS, but of course depends on what you are doing (and you might need to readjust the thresholds?).
Hope this helps but maybe someone from the team can confirm this:)
Supplementary Strelka2: https://static-content.springer.com/esm/art%3A10.1038%2Fs41592-018-0051-x/MediaObjects/41592_2018_51_MOESM1_ESM.pdf
This note also helped, page 29 about Strelka2: https://libstore.ugent.be/fulltxt/RUG01/002/785/131/RUG01-002785131_2019_0001_AC.pdf
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