# Genome build used in FinnGen

Human reference genome build [GRCh38/hg38](https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/) is used for FinnGen genotype data. All alleles are coded according to the [GRCh38/hg38](https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/) build reference alleles, and all alternative alleles are left-aligned in respect to the original variant position.

Chip array datasets generated based on previous reference genome builds are lifted-over to the [GRCh38/hg38](https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/) build according to [this protocol](https://www.protocols.io/view/genotyping-chip-data-lift-over-to-reference-genome-xbhfij6)

## Genotype reporting

* Imputed alleles are coded `0` or `1`, separated with ‘`|`’ (*phased*): `0` is for reference/wild type (WT) allele and `1` is for alternative allele.
* In raw chip data alleles are coded `0` or `1`, separated with ‘`/`’ (*unphased*): `0` is for reference/wild type (WT) allele and `1` is for alternative allele.

*Therefore,* genotypes can be of the form:

**Post-Imputation Genotype Files (phased):**

* `0|1` or `1|0` heterozygotes
* `1|1` homozygotes
* `0|0` WT homozygotes
* `.|.` missing data

**Raw Chip data (unphased)**

* `0/1` heterozygotes
* `1/1` homozygotes
* `0/0` WT homozygotes
* `./.` missing data

[Click here to read how to work with variant level data in the Sandbox](/working-in-the-sandbox/working-with-genotype-data.md)


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