We can use the tool picard to liftOver VCF file by batch
URL:
http://broadinstitute.github.io/picard/command-line-overview.html#LiftoverVcf
create dictionary (optional)
if you do not have the dict of reference fasta, you need to create first
java -jar /software/picard-tools-2.8.1/picard.jar CreateSequenceDictionary REFERENCE=/software/GATK_files/hg38/hg38.fa OUTPUT=/software/GATK_files/hg38/hg38.dict
download the chain file
Go the http://hgdownload.cse.ucsc.edu/downloads.html#human and download from liftOver hyperlink
liftOver
java -jar /software/picard-tools-2.8.1/picard.jar LiftoverVcf I=input.vcf O=lifted_over.vcf CHAIN=/software/liftOver/hg19ToHg38.over.chain.gz REJECT=rejected_variants.vcf R=/software/GATK_files/hg38/hg38.fa
Reference:
Chain format
URL: https://genome.ucsc.edu/goldenpath/help/chain.html
GENOME 101 