I’m getting NA when lifting rs11672691 from 19:41985587 on grch37 to grch38, even though it appears to be well-defined: https://www.ncbi.nlm.nih.gov/snp/rs11672691#variant_details. I’m able to lift 19:41985586 and 19:41985588 over to grch38.
What chain file are you using?
I’m using gs://hail-common/references/grch37_to_grch38.over.chain.gz, which I saw in the documentation. Is this correct?
This locus must be unmapped in the chain file – unfortunately not super uncommon. Our chain file was the latest recommended by htsjdk/samtools about 5 years ago, but I’m not sure if there’s a newer/better one available.