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What is the difference between SplitVcfs (Picard) and SelectVariants?

nithanitha indiaMember

Hi all,

Usually I do splitting SNPs and INDELs from VCF file using "gatk SelectVariants" for SNPs --select-type-to-include SNP and Indels --select-type-to-include INDEL. Accidentally I came to see the module "SplitVcfs (Picard)", which does same function like SelectVariants by splitting SNP and Indels.

Could anyone help me understands what is exact difference of the two modules. In case if I have to split SNPs and Indels from vcf file, which is the best module to use? whether the SplitVcfs module is still in use?

Version: GATK_4.1.2.0

Thanks in advance.

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  • nithanitha indiaMember
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