jvarkit

Bam2Raster

BAM to raster graphics

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar bam2raster  [options] Files

Usage: bam2raster [options] Files
  Options:
    -clip, --clip
      Show clipping
      Default: false
    -depth, --depth
      Depth track height.
      Default: 100
    --groupby
      Group Reads by. Data partitioning using the SAM Read Group (see 
      https://gatkforums.broadinstitute.org/gatk/discussion/6472/ ) . It can 
      be any combination of sample, library....
      Default: sample
      Possible Values: [readgroup, sample, library, platform, center, sample_by_platform, sample_by_center, sample_by_platform_by_center, any]
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --highlight
      hightligth those positions.
      Default: []
    --mapqopacity
      How to handle the MAPQ/ opacity of the reads. all_opaque: no opacity, 
      handler 1: transparency under MAPQ=60
      Default: handler1
      Possible Values: [all_opaque, handler1]
    --limit, --maxrows
      Limit number of rows to 'N' lines. negative: no limit.
      Default: -1
    -minh, --minh
      Min. distance between two reads.
      Default: 2
    -N, --name
      print read name instead of base
      Default: false
    --noReadGradient
      Do not use gradient for reads
      Default: false
    -nobase, --nobase
      hide bases
      Default: false
    -o, --output
      Output file. Optional . Default: stdout [20180829] filename can be also 
      an existing directory or a zip file, in witch case, each individual will 
      be saved in the zip/dir.
    -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
  * -r, --region
      Restrict to that region. An interval as the following syntax : 
      "chrom:start-end" or "chrom:middle+extend"  or "chrom:start-end+extend" 
      or "chrom:start-end+extend-percent%".A program might use a Reference 
      sequence to fix the chromosome name (e.g: 1->chr1)
    -srf, --samRecordFilter
      A filter expression. Reads matching the expression will be filtered-out. 
      Empty String means 'filter out nothing/Accept all'. See https://github.com/lindenb/jvarkit/blob/master/src/main/resources/javacc/com/github/lindenb/jvarkit/util/bio/samfilter/SamFilterParser.jj 
      for a complete syntax. 'default' is 'mapqlt(1) || Duplicate() || 
      FailsVendorQuality() || NotPrimaryAlignment() || 
      SupplementaryAlignment()' 
      Default: mapqlt(1) || Duplicate() || FailsVendorQuality() || NotPrimaryAlignment() || SupplementaryAlignment()
    --spaceyfeature
      number of pixels between features
      Default: 4
    -V, --variants, --vcf
      VCF files used to fill the position to hightlight with POS
      Default: []
    --version
      print version and exit
    -w, --width
      Image width
      Default: 1000

Keywords

• bam
• alignment
• graphics
• visualization
• png

See also in Biostars

• https://www.biostars.org/p/252491

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bam2graphics/Bam2Raster.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/bam2graphics/Bam2RasterTest.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite bam2raster ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Examples

Example 1

java -jar dist/bam2raster.jar \
	-o ~/jeter.png \
        -r 2:17379500-17379550 \
        -R  human_g1k_v37.fasta \
        sample.bam

Example 2

java -jar dist/bam2raster.jar -R ref.fa -r rotavirus:150-200 data/*.bam -o out.png --limit 10 --clip  --noReadGradient  --highlight 175 

Misc

I use the UCSC/IGV color tag ‘YC’ when available (see also samcolortag)

Screenshots

Example

$ java -jar  dist/bam2raster.jar -r "scf7180000354095:168-188"   \
	-o pit.png \
	-R  scf_7180000354095.fasta  scf7180000354095.bam 
	
	

batch:

POS=1|123 2|345 3|456
IMAGES=
BAMS=	S1|f1.bam \
	S2|f2.bam \
	S3|f3.bam
	

define run
$(1)_$(3)_$(4).png: $(2)
	java -jar dist/bam2raster.jar -clip --highlight $(4)  --mapqopacity handler1 --nobase -r "chr$(3):$(4)+50"   --reference human_g1k_v37_prefix.fasta -o $$@ $$<

IMAGES+=$(1)_$(3)_$(4).png

endef

all: all2

$(eval $(foreach P,$(POS),$(foreach B,$(BAMS),$(call run,$(word 1, $(subst |, ,${B})),$(word 2, $(subst |, ,${B})),$(word 1, $(subst |, ,${P})),$(word 2, $(subst |, ,${P}))))))

all2: ${IMAGES}
	rm -f jeter.zip
	zip jeter.zip $^

screenshots

History

• 20180917 REF is now required.

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