Germline Repeat Expansion Analysis

Implementation of the repeat_analysis step

The repeat_analysis step takes as the input the results of the ngs_mapping step (aligned reads in BAM format) and performs repeat expansion analysis. The result are variant files (VCF) with the repeat expansions definitions, and associated annotations (JSON).

Stability

This step is considered experimental, use it at your own discretion.

Step Input

The repeat analysis step uses Snakemake sub workflows for using the result of the ngs_mapping step.

Step Output

For all samples, repeat analysis will be performed on the primary DNA NGS libraries separately for each configured read mapper and repeat analysis tool. The name of the primary DNA NGS library will be used as an identification token in the output file.

For each read mapper, repeat analysis tool, and sample, the following files will be generated:

{mapper}.{repeat_tool}.{lib_name}.vcf
{mapper}.{repeat_tool}.{lib_name}.vcf.md5
{mapper}.{repeat_tool}_annotated.{lib_name}.json
{mapper}.{repeat_tool}_annotated.{lib_name}.json.md5

For example, it might look as follows for the example from above:

output/
+-- bwa.expansionhunter.P001-N1-DNA1-WES1
|   `-- out
|       |-- bwa.expansionhunter.P001-N1-DNA1-WES1.vcf
|       |-- bwa.expansionhunter.P001-N1-DNA1-WES1.vcf.md5
+-- bwa.expansionhunter_annotated.P001-N1-DNA1-WES1
|   `-- out
|       |-- bwa.expansionhunter_annotated.P001-N1-DNA1-WES1.json
|       |-- bwa.expansionhunter_annotated.P001-N1-DNA1-WES1.json.md5
[...]

Global Configuration

Not applicable.

Default Configuration

The default configuration is as follows:

# Default configuration repeat_expansion
step_config:
  repeat_expansion:
    # Repeat expansions definitions - used in ExpansionHunter call
    repeat_catalog: REQUIRED
    # Repeat expansions annotations, e.g., normality range - custom file
    repeat_annotation: REQUIRED
    # Path to the ngs_mapping step
    path_ngs_mapping: ../ngs_mapping

Available Repeat Analysis Tools

The following germline repeat analysis tool is currently available:

"ExpansionHunter"

Parallel Execution

Not available.