Recommended SV caller for downstream analysis

[amrita1983]

Hi,

I have aligned nanopore (1D) data using minimap2 for a human sample.
But when I am trying to use the sorted.bam of the same for SV calling in using Sniffles, its not giving any output.
I want to know what are the SV callers that I can use for minimap bam file.

[lh3]

Sniffles would be the best. I don't know why sniffles does not work with minimap2. You have to ask their developers. Sorry. BTW, for SV calling, please use the latest master. v2.8 has a bug.

[jblamyatifremer]

To amrita1983

I tried several times (with the latest version of both progs) to use sniffles on bam from minimap2 but it did not work. Maybe i miss some commands.
In the sniffles github, they recommand NGMLR aligner even if some use of -cs tag is planned on sniffles see https://github.com/lh3/minimap2#the-cs-optional-tag
Cheers

[leila0210]

Sniffles does not work with minimap2 cause no MD strings detected, so is it possible to output MD in minimap2?

[jblamyatifremer]

+1 for Leila0210.

[lh3]

With github master, you can get the MD tag with:

minimap2 --MD

Please let me know if it works. Thank you.

[lh3]

In fritzsedlazeck/Sniffles#51, the Sniffles developers confirmed that Sniffles should work once minimap2 outputs the MD tag, though I haven't tested this myself. I am closing the issue. If you have problems, feel free to comment on this thread or open a new issue. Thank you.