MacBookPro:data garyzhubc$ CrossMap vcf hg18ToHg19.over.chain.gz VASST.vcf VASST_liftover.vcf
usage: CrossMap vcf [-h] [--chromid {a,s,l}] [--no-comp-alleles] [--compress]
                    input.chain input.vcf refgenome.fa out_vcf
CrossMap vcf: error: the following arguments are required: out_vcf
MacBookPro:data garyzhubc$ CrossMap vcf hg18ToHg19.over.chain.gz VASST.vcf hg19.fa VASST_liftover.vcf
2025-10-12 02:17:46 [INFO]  Read the chain file "hg18ToHg19.over.chain.gz" 
2025-10-12 02:17:46 [INFO]  Filter out variants [reference_allele == alternative_allele] ...
2025-10-12 02:17:47 [INFO]  Updating contig field ... 
2025-10-12 02:17:47 [INFO]  Lifting over ... 
2025-10-12 02:18:19 [INFO]  Total entries: 1154420
2025-10-12 02:18:19 [INFO]  Failed to map: 1001
MacBookPro:data garyzhubc$ ./plink2 --vcf VASST_liftover.vcf --export bgen-1.2 bits=8 --out VASST_liftover
PLINK v2.0.0-a.7 64-bit (7 Jul 2025)               cog-genomics.org/plink/2.0/
(C) 2005-2025 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to VASST_liftover.log.
Options in effect:
  --export bgen-1.2 bits=8
  --out VASST_liftover
  --vcf VASST_liftover.vcf

Start time: Mon Oct 13 14:10:33 2025
16384 MiB RAM detected; reserving 8192 MiB for main workspace.
Using up to 16 threads (change this with --threads).

Error: Invalid alternate allele on line 119 of --vcf file.
End time: Mon Oct 13 14:10:33 2025