SnpSift Split - SnpEff & SnpSift Documentation
Author: Pablo Cingolani
Description: SnpEff and SnpSift documentation

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# SnpSift Split

Simply split (or join) VCF files. Allows to create one file per chromosome or one file every N lines.

A typical usage for this command is to:

1. Split very large VCF files `SnpSift split huge.vcf`
2. Perform some CPU intensive processing in parallel using several computers or cores
3. Join the resulting VCF files `SnpSift split -j huge.000.vcf huge.001.vcf huge.002.vcf ... > huge.out.vcf`.

E.g.: Splitting a VCF having human variants:

    java -jar SnpSift.jar split myHugeVcf.vcf.gz

Will create files myHugeVcf.1.vcf, myHugeVcf.2.vcf, ... , myHugeVcf.22.vcf, myHugeVcf.X.vcf, myHugeVcf.Y.vcf

You can also specify '-l' command line option to split the file every N lines.

E.g.: Split a VCF file every 10,000 lines:

    java -jar SnpSift.jar split -l 10000 myHugeVcf.vcf.gz

Will create files myHugeVcf.001.vcf, myHugeVcf.002.vcf, ...

Info

VCF header will be added to each file, so resulting files will be more than 10,000 lines.

You can use `-j` (join) command line option to join a set of VCF files.

    java -jar SnpSift.jar split -j huge.000.vcf huge.001.vcf huge.002.vcf ...  > huge.out.vcf