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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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Polyploidy #220

Open goeckeritz opened 12 months ago

goeckeritz commented 12 months ago

Hi Brentp,

I have a sample that's triploid. Any plans to allow smoove to be able to given a ploidy before calling?

brentp commented 12 months ago

Hi, that probably won't be officially supported, but I think it might mostly work as-is. It will be less sensitive since only 1/3 of the reads will support an event (ideally) as opposed to 1/2.

goeckeritz commented 12 months ago

Gotcha. Mostly I just think it would need to be able to make more than 2 calls per site. Is there a way to keep multi-mappers (reads containing the XA tag) when running smoove? Since I'm working with a polyploid, a lot of reads map to more than one region. I would just like to use the best mapping, even if it does map twice... any chance I can tell smoove not to drop XA reads?

brentp commented 12 months ago

Hi, smoove doesn't look at the XA tag (and discards reads with mapping-quality of 0), only the SA tag, you'd have to do some pre-processing before sending to smoove for this to work.