54gene-wgs-germline
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Overview
Installation
Configuration
Execution
Investigate the results
Tests
Core pipeline
Changelog
For developers
References
54gene-wgs-germline
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54gene Whole Genome Sequencing Germline Calling Pipeline
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54gene Whole Genome Sequencing Germline Calling Pipeline
Documentation of WGS variant calling at
54gene
Overview
Inputs
Outputs
Installation
Obtain a copy of this workflow
Install the run-time environment
Configuration
Configuration file
Manifest file
Intervals file
Sex linker file
MultiQC configuration
Config parameters
Execution
Deploying the pipeline
Wrapper scripts
Automatic retries with scaling resources
Logging
Investigate the results
Assessing completion
Outputs and results
QC
Tests
Unit tests
Pipeline/Integration tests
Snakemake unit tests
CI/CD
Core pipeline
Pulling in resources
FastQC and read trimming
Read alignment, deduplication, and BQSR
Variant calling
Joint genotyping
Variant filtering
Post-calling QC
Changelog
[1.0.0] - 2022-08-01
For developers
Contribute back
Obtain updates from upstream
References
Read the Docs
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