Hello,

I have bam files and I need to convert it to wig format to be like this:

variableStep chrom=chr2
300701 12.5
300702 12.5
300703 12.5
300704 12.5
300705 12.5

I know that there is an options in samtools called: pileup or mpileup, but it doesn't work well with me for the following reason:

if only some nucleotides of a read is mapped to a genome, it reports coverage equally to all nucleotides of that read. I need to report only coverage for mapped nucleotides within the read, do u know any other tool that make this?

Thanks,