Jared Simpson
Jared Simpson
As far as I know there isn't a dedicated tool to call somatic mutations from nanopore reads.
Hi @marcotoffoli, Yes, this is a limitation in the way nanopolish internally stores variants that I recently discovered after a discussion with another user. It will be somewhat difficult to...
Ok, I'm glad it is working after editing the reference.
Hi, That likely means it is waiting on I/O. If you leave it for awhile does it make any progress? Jared
One possible workflow is to call variants with `nanopolish variants`, then calculate read support using `phase-reads`. That is a bit roundabout though. If I add this to `nanopolish variants` what...
Hi, I'm going to make the next release after I merge in the `methylation_bam` branch, which I expect to do in the next week or two. Jared
Hi @sbridgett, There is no difference between 0.13.2 and 0.13.3 with respect to variant calling, so I suspect it isn't the cause of this issue. My first guess is that...
Nanopolish always reads the fast5 files, in this case it uses the index files for the fastq to determine which ones to load. Jared > On Dec 14, 2021, at...
Thank you for the detailed report, and for pointing out the path in the comment I linked to is incorrect, I have fixed that. One of the differences between 0.13.2...
Yes, I'll try to do this. Thanks for the reminder.