Closed kane9530 closed 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.
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
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.
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.