mop

Simple tool for capturing alignment regions with sufficient quality for genotyping.

This script has only been tested on Unix systems.

Requires Python3 with libraries: argparse, numpy os, re, io, subprocess. Requires fully installed version of samtools with the depth utility.

Assumes all input bam files in the required bamlist were aligned to the same reference genome. Using indexed bams is encouraged and required for using --POSITIONS_STRING

Installation

pip install mop-bam

Run the following command to see usage options:

mop -h

which returns:

usage: mop [-h] [-c] [-s] [--pixy_mode] [-M MEAN_DEPTH_MIN] [-x MAX_DEPTH] [-i MIN_DEPTH] [-m DEPTH_PROPORTION] [-Q MAP_QUALITY] [-q BASE_QUALITY] -b [BAMLIST]
           [-l POSITIONS_FILE] [-R POSITIONS_STRING]

Produces bedfile of genomic locations that did or did not map reads sufficiently well. Regions are written to standard out.

optional arguments:
  -h, --help            show this help message and exit
  -c, --single_sites    Output every base separately instead of joining contiguous regions (ignored with pixy_mode).
  -s, --bad_sites       Switch to return sites which fail thresholds. Default is to return passing sites (ignored with pixy_mode).
  --pixy_mode           Switch to produce output for pixy (reports every site and the number of individuals with passing quality thresholds).
  -M MEAN_DEPTH_MIN, --mean_depth_min MEAN_DEPTH_MIN
                        Minimum mean depth across all individuals.
  -x MAX_DEPTH, --max_depth MAX_DEPTH
                        Maximum number of bases allowed per individual after accounting for low base and mapping quality. This flag should always be used in conjunction with
                        -m (ignored with pixy_mode).
  -i MIN_DEPTH, --min_depth MIN_DEPTH
                        Minimum number of bases required per individual after accounting for low base and mapping quality. This flag should always be used in conjunction with
                        -m.
  -m DEPTH_PROPORTION, --depth_proportion DEPTH_PROPORTION
                        Minimum proportion of individuals with site counts greater than --min_depth that are required for site to pass. Test is applied after accounting for
                        low base and mapping quality.
  -Q MAP_QUALITY, --map_quality MAP_QUALITY
                        Minimim mapping quality.
  -q BASE_QUALITY, --base_quality BASE_QUALITY
                        Minimim base quality.
  -b [BAMLIST], --bamlist [BAMLIST]
                        List of bam files. One per line.
  -l POSITIONS_FILE, --positions_file POSITIONS_FILE
                        Optional file of reference position to pass to "samtools depth".
  -R POSITIONS_STRING, --positions_string POSITIONS_STRING
                        Optional file of reference position to pass to "samtools depth". Requires input bam files to be indexed. Format is chromosome:start-end.