FixItFelix and Variant Calling

Pipeline Version	Date Updated	Documentation Author	Questions or Feedback
aou_9.0.1	January, 2026	WARP Pipelines	File an issue

Introduction to the FixItFelix and Variant Calling workflow

FixItFelixAndVariantCall performs CMRG-focused read extraction/remapping and variant calling on corrected alignments. It subsets the input alignment to true/false-duplication intervals, remaps reads against a masked GRCh38 reference with FixItFelix, and calls variants in true-location intervals.

The workflow supports either standard VCF output or optional gVCF output (via generate_gvcf=true).

Quickstart table

Pipeline Feature	Description	Source
Analysis type	CMRG remapping + variant calling
Workflow language	WDL 1.0	openWDL
Genomic reference sequence	Masked GRCh38 (default inputs provided)
Data input file format	CRAM/BAM + reference + interval BEDs
Data output file format	VCF or gVCF (.vcf.gz / .g.vcf.gz) + index
Primary software	GATK + FixItFelix + samtools + bwa	GATK

Set-up

FixItFelix and Variant Calling installation and requirements

The workflow code can be downloaded by cloning the WARP GitHub repository. For the latest release, please see the FixItFelixAndVariantCall changelog.

The pipeline can be deployed using Cromwell, a GA4GH-compliant workflow management system.

Inputs

Input descriptions

Input variable name	Description	Type
cram_file	Input alignment file (CRAM/BAM).	File
cram_file_index	Index for cram_file (.crai/.bai).	File
original_ref_fasta	Reference fasta used for the original alignment.	File
original_ref_fasta_index	FASTA index for original reference.	File
original_ref_dict	Sequence dictionary for original reference.	File
masked_ref_fasta	Masked GRCh38 reference for FixItFelix remapping.	File
masked_ref_fasta_index	FASTA index for masked reference.	File
masked_ref_dict	Dictionary for masked reference.	File
masked_ref_amb	BWA index .amb for masked reference.	File
masked_ref_ann	BWA index .ann for masked reference.	File
masked_ref_bwt	BWA index .bwt for masked reference.	File
masked_ref_pac	BWA index .pac for masked reference.	File
masked_ref_sa	BWA index .sa for masked reference.	File
true_locations_intervals	BED of true genomic locations used for final variant calling.	File
false_duplications_intervals	BED of false-duplication locations.	File
combined_true_false_intervals	BED combining true + false regions for read extraction/remapping.	File
generate_gvcf	Emit gVCF instead of VCF. Default: false.	Boolean

FixItFelix and Variant Calling tasks and tools

The workflow runs three tasks in sequence.

1. Subset alignment to CMRG-relevant intervals
2. Remap extracted reads with FixItFelix
3. Call variants on corrected BAM

Task name and WDL link	Tool	Software	Description
subset_cram	GATK PrintReads	us.gcr.io/broad-gatk/gatk:4.4.0.0	Subsets input alignment to combined true/false intervals and outputs BAM.
FixItFelix	FixItFelix	gcr.io/broad-dsde-methods/fixitfelix:1	Extracts and remaps read pairs to masked GRCh38 reference.
call_variants	GATK HaplotypeCaller + SelectVariants	us.gcr.io/broad-gatk/gatk:4.4.0.0	Calls variants in true-location intervals and optionally filters non-variant records for VCF mode.

1. Subset alignment to CMRG-relevant intervals

subset_cram extracts reads overlapping combined_true_false_intervals to produce a smaller BAM for downstream remapping.

2. Remap extracted reads with FixItFelix

FixItFelix remaps extracted read pairs against the masked reference and outputs coordinate-sorted/indexed BAM.

3. Call variants on corrected BAM

call_variants runs HaplotypeCaller in DRAGEN mode over true-location intervals and emits either gVCF or filtered VCF.

Outputs

Output variable name	Filename, if applicable	Output format and description
output_vcf	filtered_<sample>.vcf.gz or <sample>.g.vcf.gz	Final called variants (VCF or gVCF depending on generate_gvcf).
output_vcf_index	filtered_<sample>.vcf.gz.tbi or <sample>.g.vcf.gz.tbi	Tabix index for output_vcf.
output_pipeline_version	aou_9.0.1	Workflow version string output.

Versioning

All FixItFelixAndVariantCall releases are documented in the changelog.

Feedback

Please help us make our tools better by filing an issue in WARP; we welcome pipeline-related suggestions or questions.