I am interested in calling Illumina errors. Therefore, I need to output variants with such a low support as a single read. I am using Naive Variant Caller and most of the time I get VCF file as expected. However, there are peculiar regions for which NVC reports empty VCF file such as this region: 8:4808752-4808776
Please see my Galaxy history here: https://usegalaxy.org/u/bio-g/h/monikanvc
I also tried options -q 0 -m 0 --allow_out_of_bounds_positions -t uint64 in the command line version of the tool, but the resulting VCF file is still empty and only header is included.
I checked and there is sufficient coverage in this region (using samtools tview) and there are no stretches of NNNs. Moreover, mpileup does produce some output, while NVC does not. Has this happened to anyone else? Dd you please have any advice what to try?