Recommendation of QUAL?

[greekkey]

Hi, does QUAL here has the same meaning as QUAL in SNV calling, and is there any specific recommended threshold of QUAL for filtering low quality SVs called by SvABA?

[walaj]

There are a few error modes that could pass through low quality events. The main one is DSCRD, which are events found only with discordant reads and not sequence assembly. The QUAL score can help too, and this can be tuned to the place on the ROI curve you need for your application. At least 40 for a 30x or greater genome seems like a reasonable start.

…

On Dec 15, 2021, at 2:36 AM, greekkey ***@***.***> wrote:  Hi, is there recommended threshold of QUAL for filtering low quality SVs called by SvABA? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

[dannyjomaa]

Hello, I was hoping to ask a similar question regarding QUAL values. If I understand correctly, low QUAL values aren't necessarily filtered out by SvABA if they pass other filters, is that correct? However, if I have calls where FILTER = PASS but QUAL = 0 (or otherwise has low values < 40 for the 30x sequencing data I have), would you recommend removing these calls from further analysis?