Unclear modkit pileup `--region`

[Ge0rges]

Hi Art,

To pileup many different contigs I thought of doing modkit pileup --region contig_1,contig_2 since the documentation says Commas are allowed. But that seems to not be correct? I get Error! missing contig.

I can bypass this with the --include-bed option but was wondering. Thanks!

[ArtRand]

Hello @Ge0rges,

You can only do one region at a time with --region, I should revise the help string to say "Commas are allowed in the genome coordinates" e.g. "chr20:62,141,748-62,145,077". I found this to be convenient when copy-pasting from IGV, maybe just me though. Some other programs don't seem to let you do this. If you want to use multiple regions, you need to use --include-bed. Maybe I'll add a --regions option.

[Ge0rges]

Thanks, that's reasonable. I just used --include-bed