The frontline support team will be offline as we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and available to answer questions on the forum on March 25th 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?