Bed File Of Mapq Sliding Window On A Bam File?

There may already be a recipe for this, so asking first before reinventing the wheel: I would like to create a bed file where the score is the average mapQ from the reads of the input.bam file. I think bedtools or bedops are the way to go:http://bedtools.readthedocs.org/en/latest/content/tools/bamtobed.htmlhttp://bedops.readthedocs.org/en/latest/content/reference/file-management/conversion/bam2bed.html Other than simply running bamtobed/bam2bed, I would like to be able to define a sliding window size and step for the windows, of say, size=1000 and step=200. I also would like to generate the bam2bed information only from a list of regions in regions.bed. E.g., something like:mapq_sliding_windows --bam input.bam --wsize 1000 -wstep 200 --regions regions.bed > mapq_sliding_windows.bed EDITED: Thank you Aaron for you answer. I got it working but it's slow for my 30x WGS bams: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select chrom, size from hg19.chromInfo" > hg19.genome bedtools makewindows -g hg19.genome -w 1000 -s 200 > hg19.windows.bed bedtools map -a hg19.windows.bed -b <(bedtools bamtobed -i input.bam | grep -v chrM) -c 5 -o mean &gt ...