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