Andrew Beggs

NanoSV doesn't play nicely with guppy BAM file output

3

Hi For reasons that escapes me, the current pipeline that uses minimap2 to align during guppy basecalling seems to emit an AL tag instead of the SM tag when producing...

Error at Haplotag BAM step

5

Hi Thank you for this important piece of software. Using fresh pull of singularity image for ClairS-TO, but at the haplotagging stage get the output below. I've made sure I...

Crash on SNV module

3

First attempt since my last round of queries... running with Clair3 SNVs and get: ``` Traceback (most recent call last): File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/bin/spectre", line 8, in sys.exit(main()) File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/spectre.py", line 614,...

Feature Request - tumour-normal calling

2

Hi Fritz Would be great if Spectre could support Tumour-Normal input! Thanks Andrew

Needs Bioperl to compile properly

1

Hi Jared Thanks very much for this, looks great. Struggled to compile it with our default HPC setup, seems to need Bioperl so when I added this into the module...