jvarkit

SortVcfOnRef2

Last commit

Sort a VCF using the internal dictionary or an external reference order (Deprecated: use picard SortVcf).

DEPRECATED

use picard sortvcf

Usage

Usage: sortvcfonref2 [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --maxRecordsInRam
      When writing  files that need to be sorted, this will specify the number 
      of records stored in RAM before spilling to disk. Increasing this number 
      reduces the number of file  handles needed to sort a file, and increases 
      the amount of RAM needed
      Default: 50000
    -o, --output
      Output file. Optional . Default: stdout
    -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
    --tmpDir
      tmp working directory. Default: java.io.tmpDir
      Default: []
    --version
      print version and exit

Keywords

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew sortvcfonref2

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

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/sortvcfonref/SortVcfOnRef2.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite sortvcfonref2 ? 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

Deprecated

Use picard SortVcf http://broadinstitute.github.io/picard/command-line-overview.html#SortVcf.

Example

cat input.vcf |\
   java -jar dist/sortvcfonref2.jar  -R ref.fa |\
   bgzip -c > result.vcf.gz && \
   tabix -p vcf -f result.vcf.gz