bedtools2-24.0 error

[cmccabe]

Not sure what this error is. Would the bed file being used cause this? Thank you

cmccabe@DTV-A5211QLM:~/Desktop/NGS$ coverageBed -hist -d -abam /home/cmccabe/Desktop/NGS/pool_I_090215/IonXpress_008_150902_newheader.bam -b /home/cmccabe/Desktop/NGS/bed/sorted_unix_5column_xgen_targets.bed > /home/cmccabe/Desktop/NGS/pool_I_090215/output.bam.hist.txt

***** ERROR: -counts, -d, -mean, and -hist are all mutually exclusive options. *

Bed file

chr1	955542	955763	+	AGRN:exon.1
chr1	957570	957852	+	AGRN:exon.2
chr1	976034	976270	+	AGRN:exon.2;AGRN:exon.3;AGRN:exon.4

[GenoMax]

As the error says, you are trying to use options that are incompatible (can't be used) with each other.

[cmccabe]

Strange that same command used to work in v. 2.20. Thank you .

Basically, I am just trying to get the counts per base in the bam.

So maybe I do not need the -hist option?

[cmccabe]

I did the below command to output the per base coverage per target::

coverageBed -hist -abam /home/cmccabe/Desktop/NGS/pool_I_090215/IonXpress_008_150902_newheader.bam -b /home/cmccabe/Desktop/NGS/bed/sorted_unix_5column_xgen_targets.bed > /home/cmccabe/Desktop/NGS/pool_I_090215/output.bam.hist.txt

output.bam.hist.txt

chr1    14251    14393    X28LU:04862:12482    0    +    14251    14393    0,0,0    1    142,    0,    0    142    142    1.0000000
chr1    16224    16400    X28LU:08504:06628    0    -    16224    16400    0,0,0    1    176,    0,    0    176    176    1.0000000
chr1    16324    16500    X28LU:06201:09146    3    -    16324    16500    0,0,0    1    176,    0,    0    176    176    1.0000000

this output looks very different then 2.20.0 and I noticed that there is a new release 2.25.0, maybe I should use that? Thank you

The target bed looks like this, could that be part of the problem?

chr1    955542    955763    +    AGRN:exon.1
chr1    957570    957852    +    AGRN:exon.2
chr1    976034    976270    +    AGRN:exon.2;AGRN:exon.3;AGRN:exon.4
chr1    976542    976787    +    AGRN:exon.3;AGRN:exon.5

Thank you .