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2 hours ago by

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:

21:11019500:T:C

but lifts over to this:

chr21:10492957:A:G

if I use UCSC's genome browser and search that position on hg 19 and hg38, the ref allele change seems to check out:
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

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