Feature request: Request for unmapped region option

[ankit4035]

Hi,

While this tool works great for me. I was wondering if you can get it to output the entries from list which has remain unmapped.
I supplied a list of positions to extract information for. It returned all information for all those positions where reads mapped. I wanted it to include all the positions irrespective of number of reads mapped. It would be acceptable if the output shows total reads as 0 and other information as 0s.

Thanks.

[chrisamiller]

Unfortunately, this tool is not really under active development, so I think you're unlikely to get code changes that address this request. It's pretty straightforward to write a wrapper script, or use something like https://vatools.readthedocs.io/en/latest/vcf_readcount_annotator.html to annotate your VCFs

[malachig]

I have also desired this option in the past. We do have a couple people investigating a possible update. We'll keep this open to remind us that it would be nice. But yeah, for now a wrapper is the way to go.