parati

parati is an R package and command-line tool for parent-of-origin–aware haplotype inference in trio genotype data. It infers transmitted and non-transmitted parental haplotypes along autosomes using phased windows and supports downstream export to PLINK formats.

PARATI is designed for large-scale trio datasets and can be run directly from the command line or integrated into R workflows.

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Features

• Trio-aware haplotype inference (father / mother → child)
• Sliding-window–based haplotype construction
• Explicit separation of transmitted vs non-transmitted alleles
• Supports large compressed VCF files (.vcf.gz)
• Optional export to PLINK (.bed/.bim/.fam)
• Designed for reproducible and automated pipelines

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Installation

Requirements

• R ≥ 4.1

• Operating system: Linux or macOS

• External software:

  • PLINK ≥ 1.9 (required)

Required R packages

• data.table (>= 1.16.0)
• dplyr (>= 1.1.4)
• stringr (>= 1.5.1)
• optparse (>= 1.7.5)
• openxlsx (>= 4.2.7.1)
• vcfR (>= 1.15.0)
• methods

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Install from GitHub (development version)

# install.packages("devtools")
devtools::install_github("newche/parati")

Or clone manually:

git clone https://github.com/newche/parati.git
cd parati

#or
R CMD INSTALL parati_0.99.0.tar.gz

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Input data

PARATI requires two input files.

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1. Trio genotype VCF

Format

• Compressed VCF: .vcf.gz

• Standard VCF columns:

  CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT
  

• Followed by sample columns (individual IDs)

Content requirements

• Each family must contain:

  • Biological father
  • Biological mother
  • Biological child

• Autosomes only

• Biallelic SNPs only

Chromosome handling

• The VCF does not need to be chromosome-specific
• PARATI processes one chromosome at a time internally, based on the --chr argument

Sample ID rules (important)

• Sample IDs in the VCF must exactly match the IndividualID column in the family index
• Matching is case-sensitive
• Do not use underscores _ in sample IDs, to avoid parsing issues

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Recommended quality control (before running PARATI)

Although not enforced, the following QC steps are strongly recommended:

• Filter variants by:

  • Call rate
  • Minor allele frequency (MAF)

• Remove Mendelian inconsistencies within trios

• Restrict to autosomal biallelic SNPs

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Example VCF input

Below is a partial example from the simulated testing dataset Toy_TrioGenotype.vcf.gz:

#CHROM POS     ID   REF ALT QUAL FILTER INFO FORMAT 1-M  1-P  1-B  2-M  2-P  2-B
1      100000  rs1  G   T   .    PASS   .    GT     0/0  0/1  0/1  0/0  0/1  0/1
1      101000  rs2  A   C   .    PASS   .    GT     0/0  0/1  0/0  0/0  0/0  0/0
1      102000  rs3  A   T   .    PASS   .    GT     0/0  0/0  0/0  1/1  1/1  0/1
1      103000  rs4  A   G   .    PASS   .    GT     0/1  0/1  0/1  0/1  0/0  ./.
1      104000  rs5  A   G   .    PASS   .    GT     0/1  0/0  0/1  0/0  0/1  0/0
1      105000  rs6  T   C   .    PASS   .    GT     0/0  1/1  0/1  1/1  0/1  0/1
1      106000  rs7  T   C   .    PASS   .    GT     0/0  0/0  0/0  0/1  0/0  0/1
1      107000  rs8  A   C   .    PASS   .    GT     0/0  0/0  0/0  ./.  0/1  0/1
...

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2. Family index file

Format

• Excel file: .xlsx
• Must contain exactly three required columns

Column name	Description
FamilyIndex	Family ID (integer or character, e.g. 1, FAM001)
IndividualID	Individual ID, must match VCF sample name exactly
Role	Family role: F (father), M (mother), C (child)

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Example family index

FamilyIndex  IndividualID  Role
1            1-M           M
1            1-P           F
1            1-B           C
2            2-M           M
2            2-P           F
2            2-B           C
3            3-M           M
3            3-P           F
3            3-B           C
...

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Command-line usage

Rscript inst/scripts/parati.R [options]

Required arguments

Option	Description
--geno	Trio genotype VCF file (.vcf.gz)
--family	Family index Excel file (.xlsx)
--chr	Chromosome number
--out	Output directory
--plink_path	Full path to PLINK executable

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Optional arguments

Option	Default	Description
--haplen	500000	Haplotype window length (bp)
--savetemp	FALSE	Save intermediate files
--makebed	FALSE	Export PLINK bed/bim/fam

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Example run

Rscript inst/scripts/parati.R \
  --geno Toy_TrioGenotype.vcf.gz \
  --family Toy_FamilyIndex.xlsx \
  --chr 1 \
  --out results_chr1 \
  --haplen 500000 \
  --makebed TRUE \
  --plink_path /usr/local/bin/plink

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Output

parati generates:

• Per-window inferred haplotypes

• Transmitted and non-transmitted parental alleles

• Optional PLINK files:

  • .bed
  • .bim
  • .fam

Output files are organized by chromosome and haplotype window.

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License

GPL-3 + file LICENSE

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Citation

If you use parati in your research, please cite:

parati: Parent-of-origin aware haplotype inference for trio genotype data.

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Contact

For questions or issues, please open an issue on GitHub.

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