benefit of transfering hg19 vcf to hg38 vcf

Question

[Shicheng Guo]

Hi All,

I want to survey the benefit to transfer hg19 vcf to hg38 vcf?

Thanks

[German.M.Demidov]

Not sure if I understood: do you want to liftover vcf or realign bam and produce a new vcf?

Answer 1

[Ram]

What exactly are you referring to? If you liftover a VCF to a different reference genome build, there is no gain or loss as long as all positions are conserved across the two builds. Using hg38 as a reference while variant calling is quite different and possibly better than using hg19 as a reference.