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base_plot.rst

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Base track (-draw base, -bamplot base)

Layout options

image

  • -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

Base track types

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

image

$ 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

image

$ 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

image

$ 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