2. Gallery

$ bamsnap \
  -bam ./data/NA12879.bam \
  -title "NA12879 (Daughter)" \
  -pos chr10:117542948 \
  -out ./out/NATRIO_chr10_117542948.png \
  -read_group strand

$ bamsnap \
  -bam ./data/NA12877.bam \
    ./data/NA12878.bam \
    ./data/NA12879.bam \
  -title "NA12877 (Father)" "NA12878 (Mother)" "NA12879 (Daughter)" \
  -pos chr9:114786933 \
  -out ./out/NATRIO_chr9:114786933.png \
  -draw coordinates bamplot base gene \
  -bamplot coverage base read \
  -margin 50 \
  -read_group strand \
  -plot_margin_left 20 \
  -plot_margin_right 20 \
  -border

$ bamsnap \
  -bam ./data/NA12879.bam \
  -pos chr10:117542948 \
  -no_title \
  -draw bamplot \
  -bamplot coverage \
  -out ./out/NATRIO_chr10_117542948_3.png \
  -separator_height 0

$ bamsnap \
  -bam ./data/NA12879.bam \
  -pos chr10:117542948 \
  -no_title \
  -draw coordinates \
  -out ./out/NATRIO_chr10_117542948_coordinates1.png \
  -no_target_line \
  -coordinates_axisloc bottom

Color by inter-chromosomal rearrangements

$ bamsnap \
  -bam ./data/test_SV1_chr1_37775710.bam \
  -title "SVA example (chr1:37775710)" \
  -pos chr1:37775710 \
  -out ./out/test_SV1-3.png \
  -bamplot coverage read \
  -margin 1000 \
  -no_target_line \
  -read_color_by interchrom \
  -save_image_only

Deletion

$ bamsnap \
   -bam ./data/test_DEL_4_180097876_180097877.bam \
   -pos 4:180097878-180098507 \
   -margin 1000 \
   -title deletion \
   -out ./out/test_DEL_1.png \
   -refversion hg19 \
   -show_soft_clipped \
   -read_color_by interchrom \
   -save_image_only

$ bamsnap \
   -bam ./data/test_DEL_chr12_47977510_F.bam ./data/test_DEL_chr12_47977510_M.bam ./data/test_DEL_chr12_47977510_P.bam \
   -vcf ./data/test_DEL_chr12_47977510.vcf \
   -margin 1000 \
   -title "Father" "Mother" "Child" \
   -out ./out/test_DEL_chr12_2.png \
   -show_soft_clipped \
   -read_color_by interchrom \
   -read_group strand \
   -save_image_only