Add SV for Single end ONT reads

[saranya-work]

Hi Adam,

Thanks for the wonderful tool. I am trying to add a 8977 bp deletion in a BAM file aligned with ONT reads. I get the following error :

INFO 2022-08-08 14:27:09,208 chr5_70936274_70945251_DEL interval: chr5 70936274 70945251 DEL 1.0
INFO 2022-08-08 14:27:09,208 chr5_70936274_70945251_DEL length: 8977
INFO 2022-08-08 14:27:09,632 chr5_70936274_70945251_DEL discordant fraction: 1.000000
WARNING 2022-08-08 14:27:09,633 chr5_70936274_70945251_DEL discordant fraction > 0.100000 aborting mutation!

Is there a parameter that I can use for single-end reads for creating synthetic deletions?

Thanks,
Saranya

[adamewing]

Hi, If you're wanting to make mutations in a long-read genome (ONT) you could try addindel.py with the options --aligner minimap --alignopts x:map-ont --single --force and see how you go. Define the deletion you want to make as you would for an indel rather than as an SV e.g. chr5 70936274 70945251 1.0 DEL.

[saranya-work]

Thank you. Will try this.

[saranya-work]

Hello,

When I try with the option minimap, I get the following error -
ValueError: ERROR unsupported aligner: minimap
I use v1.3. Please let me know if I should pull for the latest code.

Thanks,
Saranya