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VanLoo-lab / ascat

ASCAT R package
https://www.mdanderson.org/research/departments-labs-institutes/labs/van-loo-laboratory/resources.html#ASCAT
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Question about segments file: nmajor =0 and nminor>0 #150

Closed kane9530 closed 1 year ago

kane9530 commented 1 year ago

Hi there,

I am examining the segments file from ASCAT and I found that for some regions, nmajor =0 and nminor>0. This doesn't make sense to me since I thought if there's only 1 region, then it should be assigned as nmajor by default? Could there be an explanation for how this phenomenon arose?

Thank you.

tlesluyes commented 1 year ago

Hi @kane9530,

You are right, this should be converted into nMajor>0 & nMinor=0. It was due to a rare issue where the BAF segmentation for small segments (<6 SNPs) was not forced in the 0.5-1 space so major/minor were swapped. It has been fixed in ASCAT v3.1 (commit: https://github.com/VanLoo-lab/ascat/commit/abdb5bdc98963c94610ee79b083e3b4f0a609997) and shouldn't occur anymore with the latest version. Please let me know if you still observe such an effect with a recent ASCAT version.

Cheers,

Tom.

kane9530 commented 1 year ago

Thanks a lot @tlesluyes for taking a look, and for your speedy response!

I ran ascat via nf-core/sarek v 3.1.2, and they are using using ascat v3.0.0. Glad that this issue has been caught and fixed in the latest Ascat version.

Best wishes, Kane

tlesluyes commented 1 year ago

No worries. We don't have any control over the nf-core/sarek pipeline so I recommend running the latest version of ASCAT. The commit that I mentioned in my previous post was done more than a year ago and there were several major improvements since ASCAT 3.0.0.

Closing this issue now since a fix is available.

Cheers,

Tom.