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genome / bam-readcount

Count bases in BAM/CRAM files
MIT License
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Feature request: Request for unmapped region option #62

Open ankit4035 opened 5 years ago

ankit4035 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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.