I'd like to use samtools to read a bam and output the depth for the full extent of a given chromosome, including where there are zeros. Can this be done? I've tried giving mpileup a region extending to the ends (eg. -r chrY:0-100) and I've also tried passing in a reference FASTA (which again extends to the ends) but it doesn't seem to work.
I know I can use genomeCoverageBed from bedtools for this, but I want to make use of the filtering capabilities of samtools to get a complete output with all the information I need.
Any ideas?
Peter
I know I can use genomeCoverageBed from bedtools for this, but I want to make use of the filtering capabilities of samtools to get a complete output with all the information I need.
Any ideas?
Peter