I am trying DELLY v0.8.2 for the first time, using ~x40 coverage data on a plant genome. The bam file was obtained by running bwa mem, then sorting and indexing the result.
I am using default params for DELLY. My run results in a bcf file with no data (i.e. header is present, but no variants detected) and prints the following message to stdout:
I find it very unlikely that there are no SVs between my sample and the reference, so I guess something is wrong with my data or the way I use DELLY.
Any ideas on what might be going wrong?