Bedtools multicover how to submit a bam list

Question

[benoit.tessoulin]

Hi,

I'm trying to use bedtools muticov to find out Copy Number Variations among my samples, using the CANOES soft. I got many bam samples and canno't figure out how to "impute" a list of bams to bedtools multicov.

Already tried the following

``

find *.bam | xargs bedtools multicov -bed probes.bed -q 20 > canoes.reads.txt

An other way around:

find *.bam > bam.list
bedtools multicov -bams bam.list -bed probes.bed -q 20 > canoes.reads.txt

CANOES tutorial suggests the following form, but I can't understand how a quote around bam list could enhance things.

bedtools multicov -bams `cat bamlist.txt` -bed probes.bed -q 20 > canoes.reads.txt

Thank you eveyone!

[GenoMax]

but I can't understand how a quote around bam list could enhance things

The ` (backtick) causes the system command to run with the output being passed to program. They are there for a reason.

[benoit.tessoulin]

Thanks I got it for the backtick, but still doesn't do the job here...

[WouterDeCoster]

And what's wrong with just following the tutorial? :-P

[benoit.tessoulin]

hehe, it doesn't work when I follow the tutorial :-P Gonna ask to bedtools team if it's bedtools' version issue. But i'm still surprised that other way around don't make it work out.