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read_quality.py

Calculate Phred quality score distribution for each position on the read.

Note

Each read should have the same (fixed) length.

Usage

read_quality.py -i input.bam -o output_prefix

Options

Option Description Default
-i, --input-file Alignment file in BAM or SAM format Required
-o, --out-prefix Prefix of output files Required
-r, --reduce Ignore nucleotides with a particular phred score occurring fewer than this many times (reduces R vector size) 1
-q, --mapq Minimum mapping quality for "uniquely mapped" 30

Output

  • prefix.qual.r — R script for generating boxplot
  • prefix.qual.boxplot.pdf — quality boxplot (if R is available)