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!