merging VCFs with non-overlapping sets of variants but partially overlapping sets of samples

Question

[raf.marcondes]

How can I merge VCFs files with non-overlapping sets of variants but partially overlapping sets of samples? For example because for a certain chromosome I only had coverage for some but not all of my samples.

I can find tools to merge VCFs with identical sets of variants but non-overlapping samples, and to merge VCFs with identical sets of samples but non-overlapping variants. But neither is really what I need.

For example, suppose I have:

1.vcf: variants 1, 2 and 3 in samples A, B, C and D

2.vcf: variants 4 and 5 in samples A and B.

Answer 1

[Pierre Lindenbaum]

use GATK _3.8_ CombineVariants. https://github.com/broadinstitute/gatk-docs/blob/master/gatk3-tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.html with

-genotypeMergeOptions UNIQUIFY >Make all sample genotypes unique by file. Each sample shared across RODs gets named sample.ROD.