Sentieon Segdup Gene Caller

Segdup Gene caller is a variant caller for genes located in segmental duplication regions that contain highly similar homologs or pseudogenes. It can leverage available long-read sequencing data to improve variant calling accuracy.

⚠️ Research Use Only Disclaimer

THIS TOOL IS FOR RESEARCH USE ONLY AND IS NOT A VALIDATED CLINICAL TEST.

The Sentieon Segdup Gene Caller has not been validated for clinical diagnostic purposes. Clinical notes and significance information provided in the output YAML files are for Educational and Informational purposes only and should not be used as the sole basis for clinical decision-making.

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Segdup caller currently supports whole-genome sequencing (WGS) paired-end short reads of 150 bp length, such as those from Illumina, Element Biosciences, MGI, and others. Sentieon provides platform-specific short-read variant calling models. For accurate copy number calling and phasing, Segdup caller recommends a minimum of 20× coverage, with 30× being ideal.

Segdup caller supports additional long-read data from PacBio HiFi or Oxford Nanopore, aligned BAM files, using the corresponding Sentieon models.

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Key Features

• Copy Number Determination: Statistical modeling to determine copy number states for each gene region using maximum likelihood optimization
• Accurate Variant Calling in Complex Regions: Specialized algorithms for genes with highly similar paralogs and pseudogenes
• Haplotype Phasing: Integrates whatshap for accurate phasing and assignment of variants to specific gene copies
• Gene conversion detection: Detects gene conversion and fusion detection for select genes
• Star allele calling: Call star alleles for CYP2D6

Supported Genes

Segdup caller currently supports the following genes and segmental duplication regions:

Region Name	Genes Encoded
SMN1	SMN1, SMN2
PMS2	PMS2, PMS2CL
CYP2D6	CYP2D6, CYP2D7
GBA	GBA1, GBAP1
STRC	STRC, STRCP1
NCF1	NCF1, NCF1B
CFH	CFH, CFHR1, CFHR2, CFHR3, CFHR4
CYP11B1	CYP11B1, CYP11B2
HBA	HBA1, HBA2

Note: Segdup caller is expanding the list of supported genes. If there are particular genes you hope to support, or you encounter any issues, please file an issue.

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Installation

To install the package from Git:

git clone https://github.com/Sentieon/segdup-caller.git
pip install ./segdup-caller

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Dependencies

• Sentieon Genomics software (version 202503 or later)
• samtools (version 1.16 or later)
• bcftools (version 1.10 or later)

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Sentieon Models

You can find a list of Sentieon models in our Sentieon models repository.

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Usage

usage: segdup-caller [-h] --short SHORT [--long LONG] --sr_model SR_MODEL
                     [--lr_model LR_MODEL] --reference REFERENCE [--genes GENES]
                     [--sample_name SAMPLE_NAME] [--sr_prefix SR_PREFIX]
                     [--lr_prefix LR_PREFIX] [--config CONFIG] --outdir OUTDIR
                     [--threads THREADS] [--version] [--keep_temp]

Targeted variant caller for genes with highly similar paralogs.

Options:

  -h, --help                Show this help message and exit

  --short SHORT, -s SHORT   Input short-read BAM or CRAM (required)

  --long LONG, -l LONG      Input long-read BAM or CRAM (optional)

  --sr_model SR_MODEL       Short read model bundle (required)

  --lr_model LR_MODEL       Long read model bundle (required if --long is provided)

  --reference REFERENCE, -r REFERENCE
                            Reference file (required)

  --genes GENES, -g GENES   List of genes to be called (comma separated).
                            If not specified, all supported genes will be called.
                            Supported genes: CFH, CFHR3, CYP11B1, CYP2D6, GBA,
                            NCF1, PMS2, SMN1, STRC, HBA

  --sample_name SAMPLE_NAME Sample name (default: SM tag in the input short-read
                            BAM file will be used)

  --sr_prefix SR_PREFIX     Short read result prefix (default: sr)

  --lr_prefix LR_PREFIX     Long read result prefix (default: lr)

  --config CONFIG           Custom gene configuration file (advanced users only)

  --outdir OUTDIR, -o OUTDIR
                            Output directory (required)

  --threads THREADS, -t THREADS
                            Number of parallel threads for gene processing
                            (default: number of available CPU cores)

  --workers WORKERS, -w WORKERS
                            Number of genes processed concurrently (default: 4)

  --version                 Show program's version number and exit

  --keep_temp               Keep temporary files for debugging

Examples

Check version:

segdup-caller --version

Calling all genes with a short-read input BAM:

segdup-caller -s $short_read_bam -r $hg38_REF --sr_model $short_read_model_bundle -o $outdir

Calling SMN1/SMN2 and CYP2D6 with a short-read input BAM:

segdup-caller -s $short_read_bam -r $hg38_REF --sr_model $short_read_model_bundle -g SMN1,CYP2D6 -o $outdir

Controlling parallelization with --workers and --threads:

# Process 2 genes concurrently, each using up to 16 threads
segdup-caller -s $short_read_bam -r $hg38_REF --sr_model $short_read_model_bundle -o $outdir --workers 2 --threads 16

# Process 8 genes concurrently, each using up to 4 threads
segdup-caller -s $short_read_bam -r $hg38_REF --sr_model $short_read_model_bundle -o $outdir --workers 8 --threads 4

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Output

Sentieon Segdup caller produces the following output:

• A YAML file containing information of analysis result, including copy number states, gene conversion events if detected, etc.
• VCF files containing variant calls for each specified gene region

Note: Clinical significance and interpretation information in the YAML output is for Educational and Informational purposes only.