I have a WGS file of 200 individuals. The file was aligned using hg19. I want to run liftover to change the coordinates to hg38
I am using vcf-liftover from here https://github.com/wtsi-team144/VCF-liftover
cat $my_wgs_vcf_file | vcf-liftover hg19ToHg38.over.chain.gz > output.vcf
the output.vcf from this file always gives me 63 individuals where 127 columns of individuals information gets lost.
Can you help with this?