TB-PROFILER DELLY ISSUE

Question

[Bhawna]

I am using tb-profiler for my amplicon dataset, in that for calling the deletion I am using delly.I am getting this error -Sample does not have enough data to estimate library parameters.

I have checked my input reference fasta file and also the input sorted bam files. They seem fine to me.

Can anyone help me with troubleshooting the error

Answer 1

[Pierre Lindenbaum]

https://groups.google.com/g/delly-users/c/2Se1VMtyfnA

Delly requires about 10,000 properly aligned pairs for every sample. That's the same for single-sample or multi-sample calling, it is a per-sample quality check. You can, of course, pool samples (merge BAMs) then Delly regards this as one sample.

[Bhawna]

Thank you!! Need to check my paired ended sample files!

[Jody Phelan]

As Pierre suggested you might not have enough reads in your bam file. I don't think amplicon sequencing can be used to look for large deletions in any case so you can disable it with --no_delly. Or you can upgrade to the latest version of tb-profiler and it will continue to run even if delly fails.