I am trying to align sample genotypes from hg19 to hg38. To do so, I am using liftover from picard on my_vcf_genotype_file (VCF file)
chainfile=hg19ToHg38.over.chain.gz java -jar picard-tools-2.5.0/picard.jar LiftoverVcf I=$my_vcf_genotype_file O=$my_vcf_genotype_file.hg38.vcf.gz C=$chain_file REJECT=trash.vcf.gz R=GRCh38.primary_assembly.genome.fa
I am getting this error
INFO 2018-07-05 18:54:28 LiftoverVcf Loading up the target reference genome. INFO 2018-07-05 18:54:48 LiftoverVcf Lifting variants over and sorting. ERROR 2018-07-05 18:54:56 LiftoverVcf Encountered a contig, chr1_KI270766v1_alt that is not part of the target reference.
Can you help me to resolve this?