jvarkit

VcfToZip

Last commit

Reads a stream of concatenated VCFs and insert them into a Zip file

Usage

Usage: vcf2zip [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output zip file.
    -p, --prefix
      Prefix all zip entries with this prefix
      Default: VCF
    -t, --title
      Try to find ##(TITLE)=abcdefghijk in the VCF header and use it as the 
      name of the inserted VCF file
      Default: <empty string>
    --version
      print version and exit

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcf2zip

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/vcfconcat/VcfToZip.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcf2zip ? 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

This tool was used to create a zip from the output of VCFburdensplitter which is a stream of VCFs.

Example


$ cat ~/input.vcf ~/input.vcf ~/input.vcf | java -jar dist/vcf2zip.jar -o jeter.zip
[main] INFO jvarkit - Command Line args : -o jeter.zip
[main] INFO jvarkit - Executing as lindenb@kaamelot-master01 on Linux 2.6.32-431.17.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_60-b27
[main] INFO jvarkit - reading concatenated vcf from stdin
[main] INFO jvarkit - VCF/vcf2zip.00001.vcf
[main] INFO jvarkit - Count: 499 Elapsed: 10 seconds(0.05%) Remains: 6 hours(99.95%) Last: 1:1431105
[main] INFO jvarkit - done: N=870
[main] INFO jvarkit - VCF/vcf2zip.00002.vcf
[main] INFO jvarkit - Count: 530 Elapsed: 10 seconds(0.05%) Remains: 5 hours(99.95%) Last: 1:1510577
[main] INFO jvarkit - done: N=870
[main] INFO jvarkit - VCF/vcf2zip.00003.vcf
[main] INFO jvarkit - Count: 530 Elapsed: 10 seconds(0.05%) Remains: 5 hours(99.95%) Last: 1:1510577
[main] INFO jvarkit - done: N=870
[main] INFO jvarkit - done. Number of VCFs:3
[main] INFO jvarkit - End JOB  [Mon May 02 12:30:24 CEST 2016] VcfToZip done. Elapsed time: 0.85 minutes.
$ unzip -t jeter.zip 
Archive:  jeter.zip
    testing: VCF/vcf2zip.00001.vcf    OK
    testing: VCF/vcf2zip.00002.vcf    OK
    testing: VCF/vcf2zip.00003.vcf    OK
No errors detected in compressed data of jeter.zip.