Low Pass WGS Imputation v1 Pipeline Overview

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Inputs and Outputs

Input Validation

Quality Control

Phasing

Imputing

Troubleshooting

A detailed description of the pipeline can be found at the WARP website.

Inputs and Outputs

Inputs

The All of Us + AnVIL Low Pass WGS Imputation pipeline expects the following user-provided inputs:

Cram Manifest

A three-column TSV file that contains a row for each cram to be imputed.  The expected headers are 'cram_path', 'cram_index_path', and 'sample_id'.

See Input Requirements to ensure your input file will be accepted and processed by the service.

Output basename

The prefix for all of the outputs' filenames. May only contain alphanumeric characters, dashes, and underscores.

Minimum imputation quality for inclusion

Optional. The minimum imputation quality (INFO) for inclusion in output VCF. Value must be between 0 and 1 (inclusive). Default is 0.0.

Description

Optional. User-provided description of the job.

Outputs

When your job is complete, you will be able to download the following output files:

Imputed multi-sample VCF file

A multi-sample VCF file containing imputed variant genotypes for all samples. The VCF includes the following annotations:

• INFO fields: 
  • AF (float): Allele Frequency for the ALT allele
  • RAF (flag): ALT allele frequency in the reference panel
  • INFO (float): IMPUTE info quality score for diploid samples
• FORMAT fields:
  • GT (string): Genotype
  • DS (float): Genotype dosage
  • GP (list of floats): Genotype posteriors

Imputed multi-sample VCF index file

The index file for the imputed multi-sample VCF

 

Imputed homozygous reference sites only VCF file

A sites only VCF that contains all sites where all samples are homozygous reference.  The VCF includes the following annotations

• INFO fields: 
  • AF (float): Allele Frequency for the ALT allele
  • RAF (flag): ALT allele frequency in the reference panel
  • INFO (float): IMPUTE info quality score for diploid samples

Imputed multi-sample VCF index index file

The index file for the imputed homozygous reference sites only VCF

Imputation QC Metrics File

A TSV file containing QC information about the Imputed multi-sample VCF file.  This file is created by using the hail sample_qc method.  A description can be found at hail sample_qc documentation.

Input Validation

The service will validate that your inputs meet all the requirements. To ensure your inputs will pass these checks, please see Input Requirements.

Imputing

Imputing is done using GLIMPSE2 using the All of Us + AnVIL reference panel.

Non Autosomal Imputing

Currently the imputation service only performs autosomal imputation (chr1-chr22).

Troubleshooting

If you have any problems running the pipeline, please refer to this Troubleshooting article.