Marek Cmero
Marek Cmero
I've also tried running a conda-installed MINTIE on a slurm cluster and I'm getting this same issue. Also tested with all bpipe versions 0.9.9.9 to 0.9.11. A [manual installation](https://github.com/Oshlack/MINTIE/wiki/Install#manual-installation) may...
Thanks @ssadedin. Any chance you could send me a binary of the master build?
@ssadedin I've managed to compile the latest bpipe successfully, but it's still giving the same qstat error. Any ideas?
Thanks Nadia, I think replacing GMAP with minimap2 could work nicely to improve the contig alignments. Happy to implement in a separate branch. As you say, validation would be a...
The fields are calculated as the number of reads supporting the breakpoint divided by the supporting plus normal (unaffected) reads for each locus (left side = vaf1 and right side...
Normal reads have to pass quite a few checks in SVclone, which leans more on the conservative side for read counting. So I'm not surprised that the counts are lower...
Yes, it will also count reads spanning the boundary.
Go with the defaults unless you have a specific reason to change them.
No, SVclone doesn't check this. This would be a good additional check but was never implemented. We assume sufficiently soft-clipped reads at the SV location support the break, but this...
Supporting reads for inversions are not counted any differently to other SVs. One noteworthy aspect of inversions however is that they create two breakpoints in opposite directions, so make sure...