jvarkit

SplitBam3

Split a BAM by chromosome group

Usage

Usage: splitbam3 [options] Files
  Options:
    --bamcompression
      Compression Level. 0: no compression. 9: max compression;
      Default: 5
    --force
      overwrite existing files
      Default: false
    -g, --groupfile
      Chromosome group file. Interval are 1 based
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -M, --manifest
      Manifest file describing the generated files. Optional
    --others
      save reads that don't belong to a group into an extra group
      Default: false
  * -o, --output
      (prefix) output directory
    --prefix
      Output file prefix
      Default: split
    -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
    --regions
      Limit analysis to this interval. A source of intervals. The following 
      suffixes are recognized: vcf, vcf.gz bed, bed.gz, gtf, gff, gff.gz, 
      gtf.gz.Otherwise it could be an empty string (no interval) or a list of 
      plain interval separated by '[ \t\n;,]'
    --samoutputformat
      Sam output format.
      Default: BAM
      Possible Values: [BAM, SAM, CRAM]
    --unmapped
      save unmapped reads into an extra group
      Default: false
    --validation-stringency
      SAM Reader Validation Stringency
      Default: LENIENT
      Possible Values: [STRICT, LENIENT, SILENT]
    --version
      print version and exit

Keywords

• sam
• bam
• split

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew splitbam3

The java jar file will be installed in the dist directory.

Creation Date

20150317

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/splitbam/SplitBam3.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 splitbam3 ? 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

Split a BAM by chromosome group. Create EMPTY bams if no reads was found for a given group.

Example

the content of ‘split_g1k_v37_01.txt’

CHROMS_01_09	1 2 3 4 5 6 7 8 9
CHROMS_10_0Y	10 11 12 13 14 15 16 17 18 19 20 21 22 X Y 
CHROMS_OTHER	MT GL000207.1 GL000226.1 GL000229.1 GL000231.1 GL000210.1 GL000239.1 GL000235.1 GL000201.1 GL000247.1 GL000245.1 GL000197.1 GL000203.1 GL000246.1 GL000249.1 GL000196.1 GL000248.1 GL000244.1 GL000238.1 GL000202.1 GL000234.1 GL000232.1 GL000206.1 GL000240.1 GL000236.1 GL000241.1 GL000243.1 GL000242.1 GL000230.1 GL000237.1 GL000233.1 GL000204.1 GL000198.1 GL000208.1 GL000191.1 GL000227.1 GL000228.1 GL000214.1 GL000221.1 GL000209.1 GL000218.1 GL000220.1 GL000213.1 GL000211.1 GL000199.1 GL000217.1 GL000216.1 GL000215.1 GL000205.1 GL000219.1 GL000224.1 GL000223.1 GL000195.1 GL000212.1 GL000222.1 GL000200.1 GL000193.1 GL000194.1 GL000225.1 GL000192.1 

split the output of bwa sampe on the fly:

bwa mem (...) | samtools sort (...) | \
java -jar dist/splitbam3.jar \
	-o TESTSPLITBAM/__GROUPID__.bam \
	-m \
	-g split_g1k_v37_01.txt 


[Fri Jul 26 13:25:56 CEST 2013] Executing as lindenb@master on Linux 2.6.32-358.6.2.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_19-mockbuild_2013_04_17_19_18-b00; Picard version: null
INFO	2013-07-26 13:25:56	SplitBam	reading stdin
INFO	2013-07-26 13:25:56	SplitBam	opening TESTSPLITBAM/CHROMS_01_09.bam
INFO	2013-07-26 13:25:57	SplitBam	opening TESTSPLITBAM/CHROMS_10_0Y.bam
INFO	2013-07-26 13:25:58	SplitBam	opening TESTSPLITBAM/CHROMS_OTHER.bam
INFO	2013-07-26 13:35:58	SplitBam	closing group CHROMS_01_09
INFO	2013-07-26 13:35:59	SplitBam	closing group CHROMS_10_0Y
INFO	2013-07-26 13:35:59	SplitBam	closing group CHROMS_OTHER
INFO	2013-07-26 13:36:00	SplitBam	closing group Unmapped
Runtime.totalMemory()=1916600320

This site is open source. Improve this page.