goleft depth sliding window analysis

[lyy005]

Hi there,
I'm using "goleft depth" for estimating the sequencing depth of sliding window (10 kb window and 2 kb step) on the genome. I tried to use bed file "--bed" with sliding window information, however, the result looks like this:

Scaffold_3 0 10000 1
Scaffold_3 2000 10000 0
Scaffold_3 4000 10000 0
Scaffold_3 6000 10000 0
Scaffold_3 8000 10000 0
Scaffold_3 10000 12000 0
Scaffold_3 10000 14000 0
Scaffold_3 10000 16000 0

So I was wondering if I use the bed file properly. My command is as follows:
goleft_linux64 depth --reference genome.fasta --prefix sample1 sample1_sorted.bam --processes 20 --windowsize 10000 --mincov 0 --bed genome.windows.bed &

Thank you for any advice on this!

YY

[brentp]

don't use goleft depth for this. use mosdepth it will be faster and easier to use.