search

cortes-ciriano-lab / savana

Somatic structural variant caller for long-read data
Apache License 2.0
43 stars 2 forks source link

ValueError raised when aligned with NGMLR #20

Open lingchenL opened 1 year ago

lingchenL commented 1 year ago

Hello,

I wanted to thank you for creating and sharing this amazing tool. I've been testing it out with different aligners, and I've encountered an error when using SAVANA with a BAM file generated from the NGMLR aligner. Here's a screenshot of the error I received:

image

I was wondering if you've seen this error before, or if you have any ideas on how to resolve it?

Thank you in advance for your help. Ling

helrick commented 1 year ago

Hi there, many apologies for my delayed response.

Unfortunately, SAVANA has not been tested on NGMLR. I will look into adding support for this aligner in future. From a quick glance, it looks like this might be arising from differences in the way supplementary alignments are reported by NGMLR.

We've tested using data aligned with minimap2 and winnowmap so would recommend realigning using one of these aligners for now.