VCF Imputation
DRAGEN v.4.0 extends the capabilities to infer bi-allelic SNP variants from low-coverage sequencing samples by packaging the GLIMPSE software (2020, Olivier Delaneau & Simone Rubinacci). The DRAGEN implementation of the GLIMPSE software allows for scalability of variant imputation by adding the following features:
| • | End-to-end pipeline, where the 3 phases of the GLIMPSE software (Chunk, Phase, and Ligate) get executed by a single command, on one chromosome or multiple chromosomes |
| • | Software supported acceleration |
The tool generates imputed variants for all samples provided in the specified regions, based on a pre-existing reference panel available for download on the Illumina DRAGEN Bio-IT Platform Product Files page.
The VCF imputation tool only supports:
| • | Input sample data generated with the DRAGEN Bio-IT platform |
| • | Human sequencing data |
The following is an example of commands to impute vcf on a single chromosome:
dragen
--enable-imputation true
--imputation-ref-panel-dir <REF_PANEL_DIR>
--imputation-ref-panel-prefix <IRPv1>
--imputation-chunk-input-region <chr22>
--imputation-phase-input-list <VCF_to_be_imputed.txt>
--imputation-genome-map-dir <MAP_DIR>
--output-directory <OUT_DIR>
--output-file-prefix <OUT_PREFIX>
