Same samples, different IDs, merge two VCFs

Question

[biologist]

I have two VCF files, one that I generated when I still had the original data and one that I generated after downloading the data from the SRA. So one file has the original IDs and the other has the IDs assigned by the SRA.

I would like to merge the two, but it isn't as simple I don't think as a bunch of sed commands to fix the IDs in one file, because they will be in a different order.

Does anyone know how to do this?

For example the IDs in one file might be R333, R334, R335, R336, but in the SRA file these same genotypes might be SRR3886 (R336) SRR3887 (R334), etc. This is just an example, not the actual SRA IDs.

Thanks :)

[Pierre Lindenbaum]

did you try vcftools or gatk to merge your vcfs ?