Dear all, this is my first post. I 'm new on NGS and I have some questions that I hope you can guide me.

I want to create a python script to calculate the coverage. But I would like an output with headers as: sampleID, gene, chr, exon, start, end, and avg cov.

For that I tried with bedtools

bedtools coverage [options] -a<BAM> -b<BED> > output.txt

With my bam file I converted in bed file using bamtobed, but I think I should do something before or while I create the bedfile.

Any idea that can help me? thanks a lot!