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walaj / svaba

Structural variation and indel detection by local assembly
GNU General Public License v3.0
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Recommendation of QUAL? #109

Open greekkey opened 2 years ago

greekkey commented 2 years ago

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 commented 2 years ago

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?

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dannyjomaa commented 2 years ago

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?