in some rare occasions lead_enrichment is NA even gnomad annotation exists

FINNGEN / autoreporting

MIT License

0 stars 1 forks source link

in some rare occasions lead_enrichment is NA even gnomad annotation exists #188

Open Fedja opened 3 years ago

Fedja commented 3 years ago

attached examples from r5 rerun for flagship missing_lead_enrich_for_arto.txt

Lipastomies commented 3 years ago

lead enrichment is calculated from the gnomad genome annotation, gs://fg-datateam-analysisteam-share/gnomad/2.1/genomes/gnomad.genomes.r2.1.sites.liftover.b38.finngen.r2pos.af.ac.an.tsv.gz

None of the variants in that list are in that annotation file. They weren't in the exome annotation file either. I suspect it is possible those variants were not lifted properly in the annotation files.