SheepwormJM

icon company SBOHVM, University of Glasgow icon location Postdoc at Glasgow studying macrocyclic lactone resistance in ruminant nematodes and mites. Site contains some helpful finished code and more chaotic notes.

Results 16 comments of SheepwormJM

Pooled samples and mosaic option

Hi, I ran the new Sniffles2 v2.7.0 with the following command on my poolseq ONT data: ``` sniffles -i $SAMPLE2_BAM --snf ${SAMPLE2_NAME}.snf -v ${SAMPLE2_NAME}.vcf --mosaic-include-germline --tandem-repeats $TANDEM_REP --reference $REF_FA --output-rnames...

Pooled samples and mosaic option

Just ran it without the mosaic combination option and the common SV above is still missing. It is a complex SV, but it is also massively increased in read coverage...

Pooled samples and mosaic option

Thanks for sticking with this Fritz! Just tried the --no-qc and got back almost all SVs the log file says it put in the snf. I can now see the...

Pooled samples and mosaic option

I think a lot of the ONT reads are quite short too, not sure if that helps pick things apart.

Pooled samples and mosaic option

Yes, not human! :) Thanks. I'll get it extracted and sent to you. Jenni

Pooled samples and mosaic option

Thanks Luis! _________________________________ Please note that I don’t expect you to read or respond to this email outside your normal working hours, or when on holiday. I will not normally...