Split VCF file

Question

[Medhat]

I downloaded HapMap vcf file for one chromosome the file size is 11 Giga I am trying to use LiftoverVcf from Picard package, but it run out of memory. I am thinking to split the 11 giga file into smaller files each is one giga any tool can do that? or is there a better Idea?

already used -Xmx200g -Djava.io.tmpdir=./mytmp

[zx8754]

Related post: How to split VCF files per variant, 1000 variants per file?

Answer 1

[Pierre Lindenbaum]

Using GATK:

• RandomlySplitVariants

This tool takes a VCF file, randomly splits variants into different sets, and writes the results to separate files. By default the tool splits the input into two new sets, but it can be made to output more than two separate call sets.