7. Read alignment track (-bamplot read)

7.1. Layout options

_images/pic_read1.png
  • -read_thickness (default=5) : read thickness (unit:px)
  • -read_gap_height (default=2) : read gap height (unit:px)
  • -read_gap_width (default=2) : min size of read gap width (unit:px)
  • -read_bgcolor (default=’FFFFFF’) : read background color
  • -read_color (default=’C8C8C8’) : read color
  • -center_line (default=false): draw center line
  • -no_target_line (default=false): do not draw target line

7.2. Read group (-read_group)

It is possible to plot the reads grouped by strand using the -read_group strand option.

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$ bamsnap \
  -bam ./data/NA12879.bam \
  -pos chr10:117542948 \
  -no_title \
  -draw bamplot \
  -bamplot read \
  -out ./out/NATRIO_chr10_117542948_6.png \
  -read_group strand
_images/NATRIO_chr10_117542948_6.png

7.3. Read color (-read_color_by)

The program provides color sets for strand and chromosomes.

7.3.1. Color by strand (-read_color_by strand)

_images/test_SV1-4.png
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$ bamsnap \
   -bam ./data/test_SV1_chr1_37775710.bam \
   -title "SVA example (chr1:37775710)" \
   -pos chr1:37775710 \
   -out ./out/test_SV1-4.png \
   -bamplot coverage read \
   -margin 1000 \
   -no_target_line \
   -read_color_by strand \
   -save_image_only

The reads color by strand can be defined using -read_pos_color and -read_neg_color options.

  • -read_pos_color (default=’FFAC9C’) : positive strand read color
  • -read_neg_color (default=’A19CFF’) : negative strand read color

7.3.2. Color by inter-chromosomal rearrangements (-read_color_by interchrom)

_images/test_SV1-3.png
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$ 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

The reads color by chromosome can be defined using -read_color_interchrom_chr1, -read_color_interchrom_chr2, .., and -read_color_interchrom_chrY options.

  • Default color codes
    • chr1: #64689b ⬅⬅⬅⬅
    • chr2: #D6503A ⬅⬅⬅⬅
    • chr3: #87AA62 ⬅⬅⬅⬅
    • chr4: #F2EB89 ⬅⬅⬅⬅
    • chr5: #597E98 ⬅⬅⬅⬅
    • chr6: #C5763E ⬅⬅⬅⬅
    • chr7: #70BFE7 ⬅⬅⬅⬅
    • chr8: #91307F ⬅⬅⬅⬅
    • chr9: #80DE6E ⬅⬅⬅⬅
    • chr10: #DCA5B5 ⬅⬅⬅⬅
    • chr11: #A35A24 ⬅⬅⬅⬅
    • chr12: #978DA0 ⬅⬅⬅⬅
    • chr13: #D16525 ⬅⬅⬅⬅
    • chr14: #DCA167 ⬅⬅⬅⬅
    • chr15: #8C79B9 ⬅⬅⬅⬅
    • chr16: #E9BD71 ⬅⬅⬅⬅
    • chr17: #4B2669 ⬅⬅⬅⬅
    • chr18: #D7E4BF ⬅⬅⬅⬅
    • chr19: #733B91 ⬅⬅⬅⬅
    • chr20: #BC2D7A ⬅⬅⬅⬅
    • chr21: #EBD176 ⬅⬅⬅⬅
    • chr22: #6E786F ⬅⬅⬅⬅
    • chrX: #D5AA00 ⬅⬅⬅⬅
    • chrY: #A9D400 ⬅⬅⬅⬅
    • other chromosome: #555555 ⬅⬅⬅⬅

7.4. Show soft clipped part (-show_soft_clipped)

_images/test_SV1-3_1.png
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$ bamsnap \
   -bam ./data/test_SV1_chr1_37775710.bam \
   -title "SVA example (chr1:37775710)" \
   -pos chr1:37775710 \
   -out ./out/test_SV1-3_1.png \
   -bamplot coverage read \
   -margin 1000 \
   -no_target_line \
   -show_soft_clipped \
   -read_color_by interchrom \
   -save_image_only

7.5. Deletion

_images/test_DEL_1.png
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$ 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

The insert size threshold between read mates to detect deletions is set by -insert_size_del_threshold (default is 1000). The color of reads for deletion is #FF0000 by default. You can change the color using -read_color_deletion option.