mapq_plotter

A script to help you visualize the distribution of MAPQ scores for the reads around a given position in your bam file. Incorporated into this FireCloud workflow: https://portal.firecloud.org/#methods/ekofman/mapq_plotting/1

Example usage at single location:

python mapq_around_locus.py --bam_file mother.bam --chromosome 20 --position 16059512 --output_dir outputs

Example usage at several locations specified in a tab-delimited file with a 'Chromosome' and 'Start' column:

python mapq_around_locus.py --bam_file mother.bam --positions_file positions.txt --output_dir outputs

Example positions.txt file contents (tab-delimited):

Chromosome Start

20 16059226

20 16061080

20 16064664

20 16067971

20 16073033

20 16078668