The frontline support team will be slow on the forum because we are occupied with a GATK Workshop on March 26th and 27th 2019. We will be back and available to answer questions on the forum on March 28th 2019.
LiftoverVCF chain file for b37 to hg38
For liftover of a b37 vcf to hg38, the gatk LiftoverVcf tool needs a chain file (b37Tohg38.chain). The documentation example uses this file but I don't see it in the GATK bundles. Is there one available? Or will the ucsc hg19Tohg38.chain file work despite the contig name difference?