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read_GC.py

Calculate the GC content distribution of mapped reads.

Usage

read_GC.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
-q, --mapq Minimum mapping quality for "uniquely mapped" 30

Output

  • prefix.GC.xls — tab-separated: GC%, read count
  • prefix.GC_plot.r — R script for GC distribution plot
  • prefix.GC_plot.pdf — GC distribution plot (if R is available)