バリアント検出アルゴリズムの向上にもかかわらず、ゲノム解析における正確なバリアントの同定には、リードレベルのデータを視覚的に確認することが重要な課題となっている。著者らは、グラフィックスライブラリとBAMインデックスを利用した効率的なBAMファイルビューアであるBamSnapを開発した。既存のビューアとは異なり、BamSnapは、トラックやレイアウトをカスタマイズして高品質なスナップショットを迅速に生成することができる。一例として、2500以上の全ゲノムに対して、1000のgenomic lociのリードレベルの画像を生成している。BamSnapは、https://github.com/parklab/bamsnapから利用できる。
https://bamsnap.readthedocs.io/en/latest/
インストール
macos10.14とubuntu18.04LTSでテストした(python3.8環境)。
依存
#pypi (link)
pip install bamsnap
#github
git clone https://github.com/parklab/bamsnap
cd bamsnap
python setup.py install
> bamsnap -h
$ bamsnap
usage: bamsnap <sub-command> [options]
bamsnap ver0.2.17 (2020-12-15): convert bam (or cram) to image
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
-bam [BAM [BAM ...]] bam or cram file(s)
-bamlist BAMLIST list file with bam (or cram) file paths
-title [TITLE [TITLE ...]]
title (name) of bam (or cram) file(s)
-no_title do not draw label.
-title_fontsize TITLE_FONTSIZE
font size of title
-pos [POS [POS ...]] genomic position (ex. 1:816687-818057, 12:7462545)
-vcf VCF list file with genomic positions with VCF format
-bed BED list file with genomic positions with BED format
-out OUT output file or title of output file
-imagetype IMAGETYPE output file type
-conf CONF configuration file
-ref REF Reference sequence fasta file (ex. hg19.fa)
-ref_index_rebuild if you want to rebuild fasta index file (.fai), when it is older than the fasta file. (Default: false)
-refversion REFVERSION
Reference version (default: hg38)
-margin MARGIN genomic margin size
-save_image_only save image only
-image_dir_name IMAGE_DIR_NAME
image directory name
-zipout make a single zip file
-separator_height SEPARATOR_HEIGHT
separator's height
-process PROCESS number of process for multi-processing (default: 1)
-draw [DRAW [DRAW ...]]
track composition (default: -draw coordinates bamplot base gene)
-bamplot [BAMPLOT [BAMPLOT ...]]
track composition of bamplot (default: -bamplot coverage base read)
-width WIDTH image width (unit:px, default: 1000)
-height HEIGHT image height (unit:px)
-bgcolor BGCOLOR background color (default: FFFFFF)
-plot_margin_top PLOT_MARGIN_TOP
top margin size of plot (default: 20)
-plot_margin_bottom PLOT_MARGIN_BOTTOM
bottom margin size of plot (default: 20)
-plot_margin_left PLOT_MARGIN_LEFT
left margin size of plot (default: 0)
-plot_margin_right PLOT_MARGIN_RIGHT
right margin size of plot (default: 0)
-border draw border in plot (default: false)
-grid GRID draw grid in plot (default: 0 (grid size))
-read_thickness READ_THICKNESS
read thickness (unit:px)
-read_gap_height READ_GAP_HEIGHT
read gap height (unit:px)
-read_gap_width READ_GAP_WIDTH
min size of read gap width (unit:px)
-read_bgcolor READ_BGCOLOR
read background color
-read_color READ_COLOR
read color
-read_pos_color READ_POS_COLOR
positive strand read color
-read_neg_color READ_NEG_COLOR
negative strand read color
-read_color_deletion READ_COLOR_DELETION
read color of deletion
-read_color_inversion READ_COLOR_INVERSION
read color of inversion
-insert_size_del_threshold INSERT_SIZE_DEL_THRESHOLD
insert size threshold for deletion (default: 1000)
-insert_size_ins_threshold INSERT_SIZE_INS_THRESHOLD
insert size threshold for insertion (default: 50)
-read_group READ_GROUP
read group
-read_color_by READ_COLOR_BY
read color by
-read_color_interchrom_chr1 READ_COLOR_INTERCHROM_CHR1
paired read color located in chromosome 1
-read_color_interchrom_chr2 READ_COLOR_INTERCHROM_CHR2
paired read color located in chromosome 2
-read_color_interchrom_chr3 READ_COLOR_INTERCHROM_CHR3
paired read color located in chromosome 3
-read_color_interchrom_chr4 READ_COLOR_INTERCHROM_CHR4
paired read color located in chromosome 4
-read_color_interchrom_chr5 READ_COLOR_INTERCHROM_CHR5
paired read color located in chromosome 5
-read_color_interchrom_chr6 READ_COLOR_INTERCHROM_CHR6
paired read color located in chromosome 6
-read_color_interchrom_chr7 READ_COLOR_INTERCHROM_CHR7
paired read color located in chromosome 7
-read_color_interchrom_chr8 READ_COLOR_INTERCHROM_CHR8
paired read color located in chromosome 8
-read_color_interchrom_chr9 READ_COLOR_INTERCHROM_CHR9
paired read color located in chromosome 9
-read_color_interchrom_chr10 READ_COLOR_INTERCHROM_CHR10
paired read color located in chromosome 10
-read_color_interchrom_chr11 READ_COLOR_INTERCHROM_CHR11
paired read color located in chromosome 11
-read_color_interchrom_chr12 READ_COLOR_INTERCHROM_CHR12
paired read color located in chromosome 12
-read_color_interchrom_chr13 READ_COLOR_INTERCHROM_CHR13
paired read color located in chromosome 13
-read_color_interchrom_chr14 READ_COLOR_INTERCHROM_CHR14
paired read color located in chromosome 14
-read_color_interchrom_chr15 READ_COLOR_INTERCHROM_CHR15
paired read color located in chromosome 15
-read_color_interchrom_chr16 READ_COLOR_INTERCHROM_CHR16
paired read color located in chromosome 16
-read_color_interchrom_chr17 READ_COLOR_INTERCHROM_CHR17
paired read color located in chromosome 17
-read_color_interchrom_chr18 READ_COLOR_INTERCHROM_CHR18
paired read color located in chromosome 18
-read_color_interchrom_chr19 READ_COLOR_INTERCHROM_CHR19
paired read color located in chromosome 19
-read_color_interchrom_chr20 READ_COLOR_INTERCHROM_CHR20
paired read color located in chromosome 20
-read_color_interchrom_chr21 READ_COLOR_INTERCHROM_CHR21
paired read color located in chromosome 21
-read_color_interchrom_chr22 READ_COLOR_INTERCHROM_CHR22
paired read color located in chromosome 22
-read_color_interchrom_chrX READ_COLOR_INTERCHROM_CHRX
paired read color located in chromosome X
-read_color_interchrom_chrY READ_COLOR_INTERCHROM_CHRY
paired read color located in chromosome Y
-read_color_interchrom_other READ_COLOR_INTERCHROM_OTHER
paired read color located in other chromosome
-show_soft_clipped show soft clipped part (default: false)
-show_hard_clipped show hard clipped part (default: false)
-show_clipped show soft and hard clipped part (default: false)
-center_line draw center line
-no_target_line do not draw target line
-base_fontsize BASE_FONTSIZE
font size of base track
-base_height BASE_HEIGHT
base track height
-base_margin_top BASE_MARGIN_TOP
top margin size of base track
-base_margin_bottom BASE_MARGIN_BOTTOM
bottom margin size of base track
-coverage_height COVERAGE_HEIGHT
coverage track height
-coverage_fontsize COVERAGE_FONTSIZE
coverage font size
-coverage_vaf COVERAGE_VAF
coverage variant allele fraction threshold (default: 0.2)
-coverage_color COVERAGE_COLOR
coverage color
-coverage_bgcolor COVERAGE_BGCOLOR
coverage track background color
-heatmap_height HEATMAP_HEIGHT
coverage heatmap height
-heatmap_bgcolor HEATMAP_BGCOLOR
coverage heatmap background color
-gene_height GENE_HEIGHT
gene track height
-gene_fontsize GENE_FONTSIZE
font size of gene track
-gene_pos_color GENE_POS_COLOR
positive strand color
-gene_neg_color GENE_NEG_COLOR
negative strand color
-coordinates_height COORDINATES_HEIGHT
coordinate height
-coordinates_fontsize COORDINATES_FONTSIZE
coordinate font size
-coordinates_axisloc COORDINATES_AXISLOC
coordinate axis location
-coordinates_bgcolor COORDINATES_BGCOLOR
coordinate background color
-coordinates_labelcolor COORDINATES_LABELCOLOR
coordinate label color
-separated_bam draw a plot for each bam
-debug turn on the debugging mode
-silence don't print any log.
テストラン
coordinate sortされたbamファイルかcramファイルを指定する。indexファイル (.bam.bai, .bai, .cram.crai, or .crai) も同じパスに存在している必要がある。ここではNA12879の１領域だけを指定している。
git clone https://github.com/parklab/bamsnap
cd bamsnap/tests/
bamsnap \
-bam ./data/NA12879.bam \
-title "NA12879 (Daughter)" \
-pos chr10:117542948 \
-out NATRIO_chr10_117542948.png \
-read_group strand
NATRIO_chr10_117542948.png
複数のbamを指定することもできる。
bamsnap \
-bam data/NA12877.bam data/NA12878.bam data/NA12879.bam \
-pos chr10:117542948 -out chr10_117542948.png -read_group strand
bamは指定した順番に縦に並ぶ。
VCFファイル（raw or gzip or bgzip compressed）を指定してバリアント領域を描画。複数の領域を描画する場合は"-out"での出力名に.pngなどをつけないことで、単一の画像を出力せず、出力ディレクトリ指定とする。
bamsnap -bam data/NA12878.bam -vcf data/multiple_variants.vcf.gz \
-out outdir
VCFでコールされた全ての領域のマッピング画像を生成するため、数が多いと時間がかかる。
出力
メモ
他にBEDファイルも指定できる。リファレンスのfastaも"-ref"で利用できる。アラインメントがずれて全てミスマッチとして描画されてしまう場合、リファレンスも指定するとずれを回避できる事があります。
上にリンクを張ったwikiには様々な描画例があります。確認して下さい。
引用
BamSnap: a lightweight viewer for sequencing reads in BAM files
Minseok Kwon, Soohyun Lee, Michele Berselli, Chong Chu, Peter J Park
Bioinformatics, Published: 08 January 2021
関連
