Beagle

https://faculty.washington.edu/browning/beagle/beagle.html

• Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Beagle 5.1 is similar to version 5.0, but includes some additional improvements that increase accuracy and reduce computation time.

Ref Panel

• GRCh38/hg38 files are available at EBI 1000 genomes ftp site at ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/GRCh38_positions/
• GRCh37/hg19 files are available at Beagle site already processed to be compatible with Beagle: http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/

$ wget -np ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/GRCh38_positions/*

Reference

https://www.protocols.io/view/genotype-imputation-workflow-v3-0-nmndc5e?version_warning=no&step=1