Skip to main content Link Menu Expand (external link) Document Search Copy Copied
PipeDev Docs

Haplotype Calling

Overview

Haplotype calling is a critical step in our pipeline, involving the identification of variants from sequenced DNA by constructing haplotypes. This step uses the Genome Analysis Toolkit’s (GATK) HaplotypeCaller, which allows for calling high-confidence variants.

Implementation

The script 07_haplotype_caller.sh is designed to manage this intensive computational task effectively, utilizing SLURM for job scheduling to handle potentially large genomic datasets.

Script Description

Configured to maximize efficiency given computational constraints:

  • Nodes: 1
  • Memory: 4G
  • CPUs per Task: 2
  • Time Limit: 48:00:00
  • Job Name: hc
  • Job Array: Capable of handling 1-68 samples concurrently.

The script begins by setting up the necessary computing environment, sourcing variables, and preparing input and output directories.

Tools Used

  • GATK (v4.4.0.0): Utilized for the HaplotypeCaller tool, which is executed under specific java options to manage memory usage and parallel processing capabilities.

Process Flow

  1. File Preparation:
    • Finds recalibrated BAM files from the previous BQSR step.
    • Each BAM file is assigned to a SLURM job based on its array task ID.
  2. Variant Calling Execution:
    • HaplotypeCaller runs with parameters to produce a genomic VCF (gVCF) for each sample, which includes variant calls along with confidence scores.
    • Outputs are genomic VCF files named after each sample, stored in the designated output directory.
  3. Optimization and Debugging:
    • Detailed logging of the script’s execution, including start and end times, input and output details, and memory settings, helps in troubleshooting and ensuring reproducibility.

Quality Assurance

This stage of the pipeline includes detailed logging and error checking to ensure that the haplotype calling process is robust against computational failures and produces reliable results.

Conclusion

The Haplotype Calling step is pivotal for identifying variants accurately, setting the stage for subsequent processes such as variant annotation and interpretation. The use of high-performance computing resources ensures that our pipeline can handle large datasets efficiently and reliably.