genomecov -d -pc -ibam showing no coverage for every position about bedtools2 HOT 2 OPEN

The FLAG column in the examples you show is 255, which means that the read and its mate are unmapped (plug in 255 here: https://broadinstitute.github.io/picard/explain-flags.html). If all alignments are "unmapped" (I don't know why), then there is no coverage, technically. genomecov requires the reads to be mapped.

from bedtools2.

Someone on StackExchanged answered my question here:

It was because I included the argument -pc, which is only for paired-end reads. The second column on the bam file I showed here is all 0, which indicates single-end reads. So I removed that argument and was able to get the tables I needed, which look like this:

chromosome      1       169
chromosome      2       169
chromosome      3       171
chromosome      4       171
chromosome      5       173
chromosome      6       178
chromosome      7       178
chromosome      8       180
chromosome      9       212
chromosome      10      212

from bedtools2.