Base coverage from Bam

[ElMichael]

Hi,
I wonder if there is any option in, e.g., samtools to display regions (positions) with the base coverage >= given threshold. Something opposite to the mpileup option (when we have positions and want to see base coverage and quality). I have very small number of reads mapped to the genome and I want to see those tens or hundreds regions covered by, at least, 10-15 reads.
Thanks.

[adamdeluca]

you could use genomeCoverageBed/Bam from bedtools with the -bg option to produce a bedgraph file, that can be filtered easily: awk '($4>-10)'

[drio]

Assuming you used (-c):

$ awk '{if ($8>4) print}' my.pileup

[ElMichael]

adamdeluca, drio, thanks a lot!

[ElMichael]

I ran genomeCoverageBed from the bedtools and it was fine. However, I noticed rather strange detail. To run genomeCoverageBed you need to provide a genome file in the following format:
<chromName><TAB><chromSize>

I work with a masked reference genome. Firstly, I provided actual sizes (number of unmasked bases + number of Ns (masked)). In addition, I also made a genome file with sizes without masked bases.
After running genomeCoverageBed with these two different genome files I got the same results.
E.g.,
chr_name 100 102 37
(that is, bases at the positions 101 and 102 on the given chr are covered with 37 reads).
I checked results using IGV, and found out they are true: the count for the bases 101 and 102 is really 37.
The question is: what is the purpose of the genome file, and why the chromSize value doesn't influence on the output (at least, it's my, perhaps, wrong impression)?