How to extract coverage of custom target regions (bed file) from a bam file?

Question

[svp]

I have a bed file and a bam file. I need to find the coverage of target intervals listed in bed file by mapping over bam file?

head target.bed
#CHR    START   END Gene
chr1    11106936    11107192    MTOR
chr1    11107388    11107655    MTOR
chr1    11108018    11108369    MTOR
chr1    11109097    11109459    MTOR
chr1    11109476    11109750    MTOR
chr1    11111018    11111177    MTOR
chr1    11112840    11113006    MTOR
chr1    11114308    11114538    MTOR
chr1    11114749    11114989    MTOR
chr1    11115312    11115590    MTOR
chr1    11116962    11117130    MTOR

Answer 1

[Fabio Marroni]

You can give a look to this related post