New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

pbmm2 to report MD tag #88

Closed

gbdias opened this issue Feb 7, 2019 · 1 comment

gbdias commented Feb 7, 2019

Hi,

Do you plan to enable additional minimap2 options in pbmm2?
Specifically, I am trying to output alignments with the --MD tag. This is required for SV calling using Sniffles. It is feasible with minimap2 but currently this option does not seem to be present in pbmm2.

Thanks,
Guilherme

Member

armintoepfer commented Feb 7, 2019

No plan on adding MD. Please use samtools calmd as postprocessing.

armintoepfer closed this as completed

NicMAlexandre mentioned this issue

[ERROR]Task Node(0-rawreads/build) failed with exit-code=1 using SLURM #109

Closed

jackhump mentioned this issue

how to add the MD in pbmm2 #382

Closed

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment