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biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
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sambamba-depth: couldn't open file #433

Closed linelieblein closed 3 years ago

linelieblein commented 4 years ago

Hi

I am using sambamba depth region to look ar read coverage at 10 bp intervals. I get an error message saying " sambamba-depth: couldn't open file or find reference" about my .bed file. It has three columns, one for chromosome, one for start of interval and one for stop of interval. I don't understand what's wrong here.

I have checked that all the pathways are correct.

Thank you

akkellogg commented 3 years ago

I had a similar issue, if your bed file has a header line, i.e. "#chrom start stop", try removing that. That seemed to be what was causing the error for me.

pjotrp commented 3 years ago

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