9. Base track (-draw base, -bamplot base)

9.1. Layout options

_images/pic_base1.png
  • -base_fontsize (default=9) : font size of base
  • -base_height (default=30) : base track height
  • -base_margin_top (default=0) : top margin size of base track
  • -base_margin_bottom (default=0) : bottom margin size of base track

9.2. Base track types

The base track has three formats which are automatically defined based on the width-span of the base.

_images/NATRIO_chr10_117542948_baseplot_ex1.png 
$ bamsnap \
  -bam ./data/NA12879.bam \
  -draw bamplot \
  -bamplot coverage base \
  -pos chr10:117542948 \
  -separator_height 0 \
  -margin 500 \
  -no_title \
  -width 700 \
  -plot_margin_top 0 \
  -plot_margin_bottom 0 \
  -out ./out/NATRIO_chr10_117542948_baseplot_ex1.png
_images/NATRIO_chr10_117542948_baseplot_ex2.png 
$ bamsnap \
  -bam ./data/NA12879.bam \
  -draw bamplot \
  -bamplot coverage base \
  -pos chr10:117542948 \
  -separator_height 0 \
  -margin 50 \
  -no_title \
  -width 700 \
  -plot_margin_top 0 \
  -plot_margin_bottom 0 \
  -out ./out/NATRIO_chr10_117542948_baseplot_ex2.png
_images/NATRIO_chr10_117542948_baseplot_ex3.png 
$ bamsnap \
  -bam ./data/NA12879.bam \
  -draw bamplot \
  -bamplot coverage base \
  -pos chr10:117542948 \
  -separator_height 0 \
  -margin 10 \
  -no_title \
  -width 700 \
  -plot_margin_top 0 \
  -plot_margin_bottom 0 \
  -out ./out/NATRIO_chr10_117542948_baseplot_ex3.png