VCFShuffle
Shuffle a VCF
Usage
Usage: java -jar dist/vcfshuffle.jar [options] Files
Usage: vcfshuffle [options] Files
Options:
--bcf-output
If this program writes a VCF to a file, The format is first guessed from
the file suffix. Otherwise, force BCF output. The current supported BCF
version is : 2.1 which is not compatible with bcftools/htslib (last
checked 2019-11-15)
Default: false
--generate-vcf-md5
Generate MD5 checksum for VCF output.
Default: false
-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, --out
Output file. Optional . Default: stdout
-N, --seed
random seed. Optional. -1 = use current time.
Default: -1
--tmpDir
tmp working directory. Default: java.io.tmpDir
Default: []
--version
print version and exit
Keywords
- vcf
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 vcfshuffle
The java jar file will be installed in the dist
directory.
Creation Date
20131210
Source code
Unit Tests
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 vcfshuffle ? 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
Example
$ java -jar dist/vcfshuffle.jar input.vcf
native alternative
bcftools view --header-only in.vcf > tmp1.vcf
bcftools view --no-header in.vcf |\
awk '{printf("%d\t%s\n",int(rand()*10000),$0);}' |\
sort -t $'\t' -k1,1n -T . |\
cut -f 1 > tmp2.vcf
cat tmp1.vcf tmp2.vcf > shuffled.vcf