Brian Haas

Are there plans to put out a new release that addresses this issue? I've encountered it on mac, but not on linux for whatever reason.

No problem. I'm glad I didn't overlook anything obvious. In the meantime, I just have a script that generates new SAM text and funnels that into samtools view to convert...

Thanks for the quick response! Here's an example: It's from the bam out option of HapotypeCaller. I guess I was pointing to the wrong code after all. Maybe it's HC...

Oh! thanks for the info. What I'm trying to do is to figure out which reads are providing evidence for variants that are reported by HC. There are some cases...

In this context, for a given mutation, there might be a hundred or so reads and each cell is only contributing one to three reads. For other mutations, maybe there's...

Sounds good! After I get this current version of the pipeline released, I'll explore this further. Maybe we could follow-up on slack, or meet up at Broad at some point...

Thanks, James! I'll check that out - I think we might be able to leverage that. best, Brian On Fri, Mar 8, 2024 at 2:38 PM jamesemery ***@***.***> wrote: >...

It looks like there's some adapters on these reads that would need to get trimmed off. I expect this could be impacting the fusion calling by STAR-Fusion. Here's an example...

I've resorted to using 'samtools fastq' instead.