Test-drive the GATK tools and Best Practices pipelines on Terra
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VCF liftover question
Dear GATK team,
My VCF was generated using GATK v3 and the hg19 reference. I'd like to compare it to the latest 1000G data, e.g. "1000G_phase3_v4_20130502.sites.vcf" from the b37 folder in the GATK ref bundle.
(Is this the right phase 3 data to use or do I need to download the original from the 1000G ftp site?)
According to this: https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_LiftoverVariants.php
I'd like to use the LiftoverVariants function to liftover my VCF to b37 ref. Is this the right thing to do? If so, can you please tell me where I can file the required chain file "liftover_hg19_to_b37.txt"?
If not, could you please recommend the right tool to liftover a VCF? It looks like there is also picard's LiftoverVcf and gatk's liftOverVCF.pl
Many thanks! Look forward to hearing form you.