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When running the LiftoverVariants command, the resulting VCF header has the old contig names (ex. b37 to hg19, chromosome one's name is still "1" rather than "chr1"). This only affects the header, while the variants themselves are successfully changed. I am running "2013.1-2.4.9-3-g512dc3e". The command I used is shown below:
<gatk> -R <human_g1k_v37>.fasta -T LiftoverVariants -V <in>.vcf -dict <hg19>.dict -o <out>.vcf -chain <b37tohg19>.chain
Thanks for your help!