NanoSV doesn't play nicely with guppy BAM file output

[adbeggs]

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 an aligned BAM file. Is there any way NanoSV can be made to not look for a SM tag. The BAM runs perfectly when I recode the header to include an SM tag

Thanks

Andrew

[DHmeduni]

Hi, Is this the reason I'm getting errors while running NanoSV with newer Minimap versions?

[adbeggs]

Yep

[DHmeduni]

Sorry, but I'm gonna bother you for one last info. Can you tell me how you change the header and the tags? I have some orphanware that only runs with older minimap version. Thanks in advance.