jvarkit

FaidxSplitter

Split bed of reference genome into overlapping parts

Usage

Usage: faidxsplitter [options] Files
  Options:
    --exclude
      A regular expression to exclude some chromosomes from the dictionary.
      Default: (chr)?(M|MT)$
    -gap, --gaps, --gap
      gap file. A bed file containing the known gaps in the genome. E.g: 
      http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz 
    -gene, --gene, --genes
      gene file. You shouldn't break a record in this file.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    -x, --overlap
      Overlap  Size. The resulting BED region should overlap with 'x' bases. A 
      distance specified as a positive integer.Commas are removed. The 
      following suffixes are interpreted : b,bp,k,kb,m,mb
      Default: 1000
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
    -w, --size
      BED Size. The genome should be split into BED of 'w' size. A distance 
      specified as a positive integer.Commas are removed. The following 
      suffixes are interpreted : b,bp,k,kb,m,mb
      Default: 1000000
    -s, --small
      If it remains 's' bases in the BED split to the end of the chromosome, 
      extends the current BED. A distance specified as a positive 
      integer.Commas are removed. The following suffixes are interpreted : 
      b,bp,k,kb,m,mb 
      Default: 1000
    --version
      print version and exit

Keywords

• vcf
• reference
• bed

See also in Biostars

• https://www.biostars.org/p/475627

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 faidxsplitter

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

Creation Date

20181011

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/FaidxSplitter.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/FaidxSplitterTest.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 faidxsplitter ? 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

Motivation

For WGS sequencing, a tool I used to split the genome and parallelize things…

Example

$ wget -q -O - "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz" | gunzip -c | cut -f 2,3,4 > jeter.gaps.txt

$ wget -q -O - "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeBasicV19.txt.gz"  | gunzip -c | cut -f 3,5,6 > jeter.genes.txt

$ java -jar dist/faidxsplitter.jar -gap jeter.gaps.txt -gene jeter.genes.txt -R src/test/resources/human_b37.dict

1	10000	177417
1	227417	267719
1	317719	471368
1	521368	1521369
1	1520369	2634220
1	2684220	3689209
1	3688209	3845268
1	3995268	4995269
1	4994269	6241184
1	6240184	7830767
(...)

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