noorsmal

Results 5 comments of noorsmal

insertions behave different with multiple sample calling

Update: I tried to run sniffles v2.0.6 for the merge to see if this would solve the issue, but this does not work with .snf files created by sniffles v2.0.3.

Too few IDs in DROP GROUP error when using external data sources

I have the same issue. I added external count files to the sampleAnnotation file and it didn't include these counts when running the drop pipeline. I have tried doing 'snakemake...

a sequence name but not an actual sequence

I had the same issue. For me it was caused by the --normalize-chrs option that changed the chromosome names from chr1 -> 1. This then caused the chromosome names not...

Do not refine deletion SV because new sequence is too long

I have the same issue with no deletions being refined by Iris even with the option --also_deletions. Did you find a way around this?

Do not refine deletion SV because new sequence is too long

I found that running it seperate for deletions with max_len_change=-0.25 instead of 0.25 works for me.