I just lifted over a VCF from hg19 to hg38 using
LiftoverVcf from GATK.
I noticed a lot of the alleles have the field
ReverseComplementedAlleles in the lifted VCF I create
For example, one record of hg19 is chrom:pos:ref:alt this:
but lifts over to this:
if I use UCSC's genome browser and search that position on hg 19 and hg38, the ref allele change seems to check out: https://genome.ucsc.edu/cgi-bin/hgGateway
Is this a pretty normal phenomenon during liftover?
Looks like it happened to about 246,033 of 247,915 of my variants