# Genotype data

Chip genotype data processing and QC Samples were genotyped with Illumina (Illumina Inc., San Diego, CA, USA) and Affymetrix arrays (Thermo Fisher Scientific, Santa Clara, CA, USA).

Genotype calls were made with GenCall and zCall algorithms for Illumina and AxiomGT1 algorithm for Affymetrix data.

Chip genotyping data produced with previous chip platforms and reference genome builds were lifted over to build version 38 (GRCh38/hg38) following the protocol described here: [dx.doi.org/10.17504/protocols.io.xbhfij6.](https://dx.doi.org/10.17504/protocols.io.xbhfij6)

## Quality control

In **sample-wise** quality control steps, individuals with ambiguous gender, high genotype missingness (>5%), excess heterozygosity (+-4SD) and non-Finnish ancestry were excluded. In **variant-wise** quality control steps, variants with high missingness (>2%), low HWE P-value (<1e-6) and low minor allele count (MAC<3) were excluded.

## Pre-phasing

Before imputation, chip-genotyped samples were pre-phased with [Eagle 2.3.5](https://data.broadinstitute.org/alkesgroup/Eagle/) using the default parameters, except the number of conditioning haplotypes, which was set to 20,000.


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://finngen.gitbook.io/documentation/methods/genotype-imputation/genotype-data.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.