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Split a BAM by chromosome group


Usage: splitbam3 [options] Files
      Compression Level.
      Default: 5
    -g, --groupfile
      Chromosome group file. Interval are 1 based
    -h, --help
      print help and exit
      What kind of help. One of [usage,markdown,xml].
    -m, --mock
      add mock record if no samRecord saved in bam
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    -u, --unmapped
      unmapped chromosome name
      Default: Unmapped
      print version and exit


Requirements / Dependencies

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.

Source code




The project is licensed under the MIT license.


Should you cite splitbam3 ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:


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. img

file output MUST contain the word ‘GROUPID


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 \
	-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