Question: Bedtools Coverage 1x Max Issue
gravatar for kerriganblake
3.8 years ago by
kerriganblake0 wrote:

I am trying to make a histogram of the sequencing depth in a set of BAM files using the WES kit's target_regions.bed file. I ran the following command with no error messages generated:

bedtools coverage -hist -abam sample.bam -b target_regions.bed | grep ^all > sample.bam.hist.all.txt

However, after running this on each of my 35 samples, all of the files show at most 1x coverage (which can be clearly demonstrated as wrong in IGV), like the following:

all     0       1644941785      -277541545      0.4094517
all     1       -1922483330     -277541545      0.5905483

I did ensure the BED file was sorted, though I noticed that the position of chrM is in a different location in my BAM and my BED. Could this cause the issue or is it something more complicated? I've been reading forums all day to no avail, so any suggestions are welcome! Thanks!

depth exome bedtools • 1.2k views
ADD COMMENTlink modified 20 months ago by melissawongukm10 • written 3.8 years ago by kerriganblake0

Did you make any progress on this problem? Currently googling and having trouble making any headway...

ADD REPLYlink written 3.6 years ago by stachele0
gravatar for melissawongukm
20 months ago by
melissawongukm10 wrote:

Hi, it seems like the bedtools command has changed. The correct command should be:

bedtools coverage -hist -a x.bed -b x.bam

Now the file should contain each feature on the bed file plus "all" lines. To make sure all lines contain 7 columns and can be read by R read.table, I added two more columns to "all" lines.

bedtools coverage -hist -a x.bed -b x.bam | awk '{if ($1=="all") print $0"\t.\t."; else print $0}' > x.hist.txt
ADD COMMENTlink modified 20 months ago by GenoMax96k • written 20 months ago by melissawongukm10
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