AGIDB: Imputation

This is a free genotype imputation and phasing service. This page provides four imputation scenarios, as follows:

► Imputation from Chip to High-coverage sequencing.

► Imputation from Low-coverage to High-coverage sequencing.

► Imputation from Chip to Chip, to realize map conversion between chips.

► Imputation of the specified map.

Imputation (Pigeon)

This module implements the imputation function from chip data to sequencing data through Beagle 5.4 software. In this module, You can upload target dataset in VCF or VCF compressed format and receive imputed and phased genomes back.

Submit the target file: e.g., VCF

Upload a VCF file

Input a genomic region:

e.g., CM053657.1:1-1000000

Input the effective population size (ne):

e.g., 100

Choose a reference panel:

AGIDB

Choose the pipeline:

phase with Beagle, no imputation

no pre-phasing, impute with Beagle

pre-phase with Beagle and impute with Beagle

Click the "Submit" button to perform imputation.

Imputation (Pigeon)

This module uses GLIMPSE2 software to implement the imputation of low-coverage sequencing reads. You only need to provide low-coverage VCF/BCF file containing the genotype likelihoods to obtain high-coverage genotype imputation files. Note: Please upload the VCF compressed format in binary format, not gzip format. Click to download the Pigeon example file: example.vcf.gz

👉Submit VCF/BCF file:

Upload a VCF/BCF file

👉Input a genomic region:

e.g., CM053657.1:1-1000000

👉Input the effective population size (ne):

e.g., 100

👉Submit:

Click the "Submit" button to perform imputation for low-coverage sequencing.