Genotype imputation workflow v3.0 v2

The actual imputation protocol begins at step 2. The actual imputation protocol begins at step 2.All consecutive steps (commands given in 'cmd COMMAND' sections) must be run to ensure All consecutive steps (commands given in 'cmd COMMAND' sections) must be run to ensure high-quality results.high-quality results.For a 'quick and dirty' genotype imputation 'run', you can jump straight to Steps 9-10 Steps 9-10 and only run these (assuming you already have all the required files in the correct format).Throughout the protocol we assume Bash shell. This Step 1Step 1 defines the requirements for the protocol (e.g.required software packages and reference genome files) and suggests example commands on how to process the files into suitable formats. In the protocol, we assume human reference genome build version GRCh38/hg38GRCh38/hg38.To lift-over and update the build of your chip data, you can use our lift-over protocol: https://www.protocols.io/view/genotyping-chip-data-reference-genome-build-lift-o-nqtddwnPlease note, that build 38 compatible VCF files should and auxiliary files might have 'chr' prefixes in chromosome names.Therefore, some minor corresponding changes might be required in the related commands to parse/work with these files correctly.If you prefer GRCh37/hg19 or other genome build versions, please download the corresponding reference genome, map and reference panel files and modify the suggested commands accordingly.1.0 Docker images and preprepared files 1.0 Docker images and preprepared filesWe have prepared docker images to ease up the preparatory steps depending on your We have prepared docker images to ease up the preparatory steps depending on your application: application: genotype-liftover-imputation-protocols-light genotype-liftover-imputation-protocols-full Light image Light image contains the software packages installed (Step 1.1), the reference genome (Step 1.2.1), genetic map files (Steps 1.2.2 and 1.2.3) and example scripts to run commands in each step (Steps 2-13).Full image Full image contains the software packages installed (Step 1.1), preprepared publically available reference files (as defined in Steps 1.2 and 1.3) and example scripts to run commands in each step (Steps 2-13).