Kieran O'Neill
Kieran O'Neill
Hi there, I'm trying to use SURVIVOR to merge matching tumour and normal vcfs generated by sniffles from PromethION data. However, this seems to be erroneously losing variants during the...
I know that @jts has been pretty involved with the development of the spec for the MM tag, and has even [mentioned getting nanopolish to work with it](https://github.com/igvteam/igv/issues/945#issuecomment-840124650). But it...
This is causing various downstream issues, as the next logical step after running SALSA is to manually edit the assembly, and juicebox seems to be the only tool to do...
Thanks again for making SALSA! I've been running it through the Docker container from Biocontainers, which autobuilds from the conda environment. This works very well for running SALSA itself, but...
[Svim](https://github.com/eldariont/svim) and [sniffles](https://github.com/fritzsedlazeck/Sniffles) are two SV callers specifically for long-read sequence data. It would be highly beneficial to be able to input them to MAVIS, both to cluster calls with...
Reading in vcfs from variant callers that run on long-read bams is only part of the problem. MAVIS still needs bam files for most operations. Such bams have a few...
Would there be any chance of getting Talon to accept bams as input? We have bams >100GB. We basically never store these as sams, since they'd be 0.5TB each. But...
Right now half of the parameters to Talon are passed directly (e.g. `--db`, `--build`), but the other half (sample info, sam file) are passed via a separate comma-separated file. This...
I'm not sure what format old Stringtie used, but Stringtie2 outputs a gtf file containing both the transcript locations and the quantities. When I try the method suggested in the...
It would be very helpful to have a reference-guided assembly available for the long-read functionality of rnabloom.