> For the complete documentation index, see [llms.txt](https://help.dragen.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.dragen.illumina.com/dragen-v4.6/product-guides/dragen-v4.6/dragen-dna-pipeline/small-variant-calling/upd-calling.md).

# UPD Caller

The Uniparental Disomy (UPD) Caller detects chromosomal regions where a child has inherited both copies of a chromosome from a single parent rather than one copy from each parent. UPD is clinically significant as it can unmask recessive disorders or disrupt imprinted gene expression.

## UPD Subtypes

| Subtype                | Description                                                              |
| ---------------------- | ------------------------------------------------------------------------ |
| **Isodisomy (ISO)**    | Both copies are identical — inherited from a single parental chromosome. |
| **Heterodisomy (HET)** | The child receives both non-identical chromosomes from one parent.       |

## Prerequisites

The UPD Caller operates on SNP genotype data from a trio (child, mother, father). The typical workflow is:

1. Run single-sample germline variant calling with gVCF output for each trio member.
2. Run the UPD Caller on the three single-sample gVCFs.

Alternatively, you can first run the Joint Genotyper and then run the UPD Caller on the resulting multisample VCF.

## Input Files

| Input                                | Format           | Description                                                                                                                                                                                   |
| ------------------------------------ | ---------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Variant VCF                          | `.vcf.gz`        | Multisample VCF, multisample gVCF, three single-sample VCFs, or three single-sample gVCFs from the Joint Genotyper or individual variant callers.                                             |
| Pedigree file                        | `.ped`           | Tab-delimited PED file: Family\_ID, Individual\_ID, Paternal\_ID, Maternal\_ID, Sex, Phenotype. Must contain exactly one family with three members.                                           |
| Cyto LOH VCF (optional, recommended) | `.vcf.gz`        | Proband cytogenetic LOH regions from the DRAGEN CNV Caller (`<prefix>.cyto.vcf.gz`). Enables deterministic disambiguation of ambiguous probes. Preferred over ROH BED when both are provided. |
| ROH BED (optional)                   | `.bed`           | Proband ROH regions from the DRAGEN ROH Caller (`<prefix>.roh.bed`). Used for disambiguation when no cyto LOH VCF is available.                                                               |
| CNV file (optional)                  | `.bed` or `.vcf` | Proband CNV calls. Masks aneuploid regions that would confound UPD detection.                                                                                                                 |

## Command-Line Options

| Option                | Description                                                                                                                                                                                                                                   | Default  |
| --------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------- |
| `--enable-upd-caller` | Enable the UPD calling pipeline.                                                                                                                                                                                                              | `false`  |
| `--pedigree-file`     | Path to a PED file identifying the trio. Must contain exactly one 3-member family.                                                                                                                                                            | Required |
| `--variant`           | Input VCF(s). Accepts a single multisample VCF, a single multisample gVCF, three single-sample VCFs, or three single-sample gVCFs. Supports `.vcf.gz` format.                                                                                 | Required |
| `--upd-loh-cyto`      | Cytogenetic LOH VCF for the proband (`<prefix>.cyto.vcf.gz`). Recommended input for disambiguation. When provided, takes precedence over `--upd-roh-bed`. Enables deterministic resolution of ambiguous probes and COMPLEX co-call detection. | Optional |
| `--upd-roh-bed`       | BED file of ROH regions for the proband (`<prefix>.roh.bed`). Used for disambiguation when `--upd-loh-cyto` is not available. Ignored if `--upd-loh-cyto` is also provided.                                                                   | Optional |
| `--upd-proband-cnv`   | BED or VCF of CNV regions for the proband. Positions overlapping these regions are excluded from UPD analysis. BED: all regions excluded with 10 kb padding. VCF: only non-copy-neutral regions (CN ≠ 2) excluded.                            | Optional |
| `--upd-include-chrx`  | Include chrX in UPD analysis. Automatically forced to `false` for male probands.                                                                                                                                                              | `true`   |

## Example Command Lines

**Using three single-sample gVCFs with cyto LOH VCF (recommended):**

```bash
dragen \
  --enable-upd-caller true \
  --variant <proband.gvcf.gz> \
  --variant <mother.gvcf.gz> \
  --variant <father.gvcf.gz> \
  --pedigree-file <family.ped> \
  --upd-loh-cyto <proband.cyto.vcf.gz> \
  --upd-proband-cnv <proband.cnv.vcf.gz> \
  --output-directory <output_dir> \
  --output-file-prefix <prefix> \
  -r <ref_dir>
```

**Using a multisample VCF from the Joint Genotyper:**

```bash
dragen \
  --enable-upd-caller true \
  --variant <joint_trio.vcf.gz> \
  --pedigree-file <family.ped> \
  --upd-loh-cyto <proband.cyto.vcf.gz> \
  --upd-proband-cnv <proband.cnv.vcf.gz> \
  --output-directory <output_dir> \
  --output-file-prefix <prefix> \
  -r <ref_dir>
```

**Excluding chrX from analysis:**

```bash
dragen \
  --enable-upd-caller true \
  --variant <proband.gvcf.gz> \
  --variant <mother.gvcf.gz> \
  --variant <father.gvcf.gz> \
  --pedigree-file <family.ped> \
  --upd-loh-cyto <proband.cyto.vcf.gz> \
  --upd-include-chrx false \
  --output-directory <output_dir> \
  --output-file-prefix <prefix> \
  -r <ref_dir>
```

**Using ROH BED when no cyto LOH VCF is available:**

```bash
dragen \
  --enable-upd-caller true \
  --variant <proband.gvcf.gz> \
  --variant <mother.gvcf.gz> \
  --variant <father.gvcf.gz> \
  --pedigree-file <family.ped> \
  --upd-roh-bed <proband.roh.bed> \
  --upd-proband-cnv <proband.cnv.vcf.gz> \
  --output-directory <output_dir> \
  --output-file-prefix <prefix> \
  -r <ref_dir>
```

## Output Files

| File                        | Description                                                                                    |
| --------------------------- | ---------------------------------------------------------------------------------------------- |
| `<prefix>.upd.vcf.gz`       | Primary output. Compressed VCF of significant UPD calls (one record per event per chromosome). |
| `<prefix>.upd.table.tsv`    | Per-chromosome raw event counts (always written).                                              |
| `<prefix>.upd.probe.bed.gz` | Per-SNP classification BED with RGB colors for genome browser visualization. Tabix-indexed.    |

### UPD VCF Output Format

Each record in the UPD VCF represents one significant UPD event on one chromosome.

**Fixed columns:**

| Column | Value                                     |
| ------ | ----------------------------------------- |
| CHROM  | Chromosome name                           |
| POS    | Start position (leftmost informative SNP) |
| ID     | `UPD:<chrom>:<start>:<end>`               |
| REF    | N                                         |
| ALT    | `<UPD>`                                   |
| QUAL   | .                                         |
| FILTER | PASS                                      |

**INFO fields:**

| Field | Description                              |
| ----- | ---------------------------------------- |
| END   | End position (rightmost informative SNP) |
| SVLEN | Length of UPD region (END − POS)         |

**FORMAT fields (proband sample only):**

| Field   | Description                                  |
| ------- | -------------------------------------------- |
| GT      | `1/1` = ISO, `0/1` = HET, `./1` = COMPLEX    |
| UPDVAR  | Number of variant sites supporting the event |
| UPDBPI  | Number of BPI sites on the chromosome        |
| UPDTYPE | `ISO`, `HET`, or `COMPLEX`                   |
| UPDPAR  | `MAT` (maternal) or `PAT` (paternal)         |
| UPDSIG  | p-value (scientific notation)                |

**Example VCF record:**

```
chr15  23450000  UPD:chr15:23450000:89000000  N  <UPD>  .  PASS  END=89000000;SVLEN=65550000  GT:UPDVAR:UPDBPI:UPDTYPE:UPDPAR:UPDSIG  1/1:847:12:ISO:MAT:3.21e-18
```

### Probe BED Output

The probe BED file classifies each informative SNP and assigns RGB colors for visualization in IGV or UCSC Genome Browser:

| Label | Event                  | Color  | RGB         |
| ----- | ---------------------- | ------ | ----------- |
| UH\_P | Paternal heterodisomy  | Pink   | 238,119,170 |
| UI\_P | Paternal isodisomy     | Green  | 34,136,51   |
| UA\_P | Paternal ambiguous     | Pink   | 238,119,170 |
| UH\_M | Maternal heterodisomy  | Blue   | 68,119,170  |
| UI\_M | Maternal isodisomy     | Purple | 136,34,85   |
| UA\_M | Maternal ambiguous     | Blue   | 68,119,170  |
| BPI   | Biparental inheritance | Gray   | 153,153,153 |

### Table Output

The table file (`<prefix>.upd.table.tsv`) contains per-chromosome raw counts:

The presence or absence of a LOH input (`--upd-loh-cyto` or `--upd-roh-bed`) determines which columns are populated:

**With LOH input (`--upd-loh-cyto` or `--upd-roh-bed`):** `pat_amb` and `mat_amb` are always zero. Ambiguous probes are deterministically resolved into heterodisomy or isodisomy counts, so `pat_hUPD` and `mat_hUPD` are non-zero wherever heterodisomy is detected.

```
chr  pat_hUPD  pat_iUPD  pat_amb  mat_hUPD  mat_iUPD  mat_amb  BPI  informative
chr1    15        8         0        12         5         0      200    240
chr2     8        4         0         7         3         0      180    202
...
```

**Without LOH input:** `pat_hUPD` and `mat_hUPD` are always zero. Heterodisomy cannot be distinguished from ambiguous signal, so all ambiguous probes are counted in `pat_amb` and `mat_amb` instead.

```
chr  pat_hUPD  pat_iUPD  pat_amb  mat_hUPD  mat_iUPD  mat_amb  BPI  informative
chr1     0        8        15        0          5        12      200    240
chr2     0        4         8        0          3         7      180    202
...
```

## LOH Input and Disambiguation

Providing a LOH input enables the caller to deterministically resolve ambiguous probes and detect COMPLEX events (co-occurring heterodisomy and isodisomy on the same chromosome). Without a LOH input, ambiguous probes contribute to both heterodisomy and isodisomy tests, and COMPLEX events cannot be called.

The recommended input is the cyto LOH VCF produced by the DRAGEN CNV Caller (`<prefix>.cyto.vcf.gz`), provided via `--upd-loh-cyto`. If this file is not available, the ROH BED from the DRAGEN ROH Caller (`<prefix>.roh.bed`) can be used instead via `--upd-roh-bed`. When both are provided, the cyto LOH VCF takes precedence and the ROH BED is ignored.

## Limitations

* The UPD Caller requires trio data (proband + both parents). It does not support duo or singleton analysis.
* ChrX is included by default but is automatically excluded for male probands.
* Segmental UPD is not supported. The caller operates at the chromosome level and requires an event to cover at least approximately 70% of the chromosome to be called. The reported start and end coordinates are anchored to the outermost supporting SNPs, potentially overestimating the true size of the UPD event.


---

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