I am trying to run the following command:
samtools bedcov test.bed /data/A.realigned.recalibrated.bam
test.bed looks like this:
track name="test bed file" chr1 20915535 20915536 chr1 20915701 20915704
The bam file has a bam.bai file in the same folder.
However I am getting this error:
Errors in BED line 'chr1 20915535 20915536' Errors in BED line 'chr1 20915701 20915704'
I am not sure what this error is. I made this bed file using tabs between columns. Appreciate your help or direction!
That happens when there are other delimiters expect tab present in the file, e.g. a whitespace somewhere. Make sure you only have tab and nothing else.
Hmm, interesting, I thought it might be that, but I am not seeing any extra chars. using ":set list" in vim shows: