Comparing VCFs constructed from mapping to different reference genomes

Question

[kat]

Hi, I am comparing variant calling pipelines from two authors who have used different versions of a reference genome. Is there a tool that could allow me to compare VCF files constructed from mapping/variant calling on two different ref genomes? Or is there a method for converting the VCF to a VCF from a different ref genome?

Thank you in advance for your help!

Answer 1

[kat]

I am responding to my own question above. I have found a Picard tool

https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.0.0/picard_vcf_LiftoverVcf.php that looks like it would allow me to "lift over" my variants onto another genome build.

Thanks!

[Begonia_pavonina]

Something is still unclear to me:

Is this tool used to compare VCF files created with different version of the same reference sequence, or can it be used with two completely different reference sequences from the same species?