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 (Water buffalo)

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:

Input the effective population size (ne):

e.g., 100

Choose a reference panel:

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 (Water buffalo)

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 Water buffalo example file: example.vcf.gz

👉Submit VCF/BCF file:

Upload a VCF/BCF file

👉Input a genomic region:

👉Input the effective population size (ne):

e.g., 100

👉Submit:

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

This module uses GLIMPSE2 software to implement the imputation of low-coverage sequencing reads. You only need to provide low-coverage BAM/CRAM files containing low-coverage sequencing reads to obtain high-coverage genotype imputation files.

👉Submit BAM/CRAM files, BAM/CRAM Index, and a BAM/CRAM list:

Please submit the BAM/CRAM files, BAM/CRAM index files and a BAM/CRAM list file containing all samples to be imputed. Supports uploading multiple BAM/CRAM files. List (.txt file) of input BAM/CRAM files containing BAM/CRAM file containing low-coverage sequencing reads. One file per line. A second column (space separated) can be used to specify the sample name. (Pig example files are provided for users to test run.)

Example file:

Upload files

👉Input a genomic region:

👉Input the effective population size (ne):

e.g., 100

👉Submit:

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

Chip version conversion (Water buffalo)

👉Submit the chip file:

In this module, users can convert the uploaded chip data to any chip version provided by this module, and the map information of all versions is available for download. Submitted text must be in VCF format. VCF format: VCF

Upload a VCF file

👉Chip version:

👉Input a genomic region:

👉Input the effective population size (ne):

e.g., 100

👉Submit and download results:

Click the "Submit" button to perform chip version conversion.

Genotype imputation to specified map (Water buffalo)

👉Submit a map file:

In this module, the user needs to submit a Map file and a VCF file. After the imputation is completed, the user will get the imputation result of the specified map. To ensure user-friendliness, it is recommended to submit map information by chromosome. Map files should contain two columns: CHROM and POS. Map format: MAP

Upload a MAP file

👉Submit the chip file:

VCF format: VCF

Upload a VCF file

👉Input a genomic region:

👉Input the effective population size (ne):

e.g., 100

👉Submit and download results:

Click the "Submit" button to get the imputation result of the specified map.