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genepi / imputationserver

Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity
https://imputationserver.sph.umich.edu/
GNU Affero General Public License v3.0
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No Variant is TYPED_ONLY #119

Open DarioS opened 11 months ago

DarioS commented 11 months ago

Neither the user guide nor the journal article explain what it means that all are IMPUTED or TYPED but none are TYPED_ONLY.

library(VariantAnnotation)
variants <- readVcf("chr10.dose.vcf.gz", param = ScanVcfParam(geno = NA))
> table(imputed = info(variants)$IMPUTED, typed = info(variants)$TYPED, typedOnly = info(variants)$TYPED_ONLY)
, , typedOnly = FALSE
       typed
imputed    FALSE     TRUE
  FALSE        0    26610
  TRUE  14186296        0

TYPED: Marker was genotyped AND imputed.

What if the array value contradicts the imputed value for a particular SNV?