Lift over to bed file only (slow running liftOver):
liftVCF.py -d 33617.vcf.gz -o 33617.scr3 -c susScr11ToSusScr3.over.chain.gz
Followed by applying to VCF file, in resume mode (fast):
liftVCF.py -d 33617.vcf.gz -o 33617.scr3 -c susScr11ToSusScr3.over.chain.gz -r -a | vcf-sort -c | bgzip > 33617.scr3.vcf.gz
Or, run both in one command,
liftVCF.py -d 33617.vcf.gz -o 33617.scr3 -c susScr11ToSusScr3.over.chain.gz -a | vcf-sort -c | bgzip > 33617.scr3.vcf.gz