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
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Bhawna •
1 answer
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.
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.
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