Test data for nf-updhmm nextflow pipeline

nf-UPDhmm Test Data and Reference Files

The dataset provided for the nf-UPDhmm pipeline includes both test VCF files and reference BED files required for preprocessing and execution.

1. Test data – VCF files

VCF files from 1000 Genomes Project. These samples were extracted from the publicly available phased SNV/INDEL VCFs release (https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/).

• mother.vcf.gz: HG00404

• father.vcf.gz: HG00403

• proband_control.vcf.gz: HG00405

• proband_heterodisomy.vcf.gz: HG00405 with a simulated heterodisomy event introduced.

Note: To ensure computational efficiency, all VCFs are restricted to this region (chr21:29222885-34430153). This allows the pipeline test to run quickly while preserving the structure of a real trio dataset.

2. Reference files – BEDs

In addition to the test VCFs, we provide BED files that define regions excluded during preprocessing. These are reference files, not test data, but they are required for the correct execution of the nf-UPDhmm pipeline.

The files are organized by reference genome version:

-prefix "hg19"

-prefix "hg38"

1. centromeres.bed

   • Centromeric and pericentromeric regions (±2 Mb).

   • Sources:

     • hg19: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz

     • hg38: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/centromeres.txt.gz

2. segmental_duplications.bed

   • Annotated segmental duplications.

   • Sources:

     • hg19: https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/genomicSuperDups.txt.gz

     • hg38: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/genomicSuperDups.txt.gz

3. hla_kir.bed

   • Highly polymorphic immune-related loci.

   • Coordinates used:

     • hg19:

       • HLA: chr6:28,477,797–33,448,354

       • KIR: chr19:55,228,188–55,383,188

     • hg38:

       • HLA: chr6:28,510,120–33,480,577

       • KIR: chr19:54,025,634–55,084,318

4. excluded_regions.bed

   • A combined file merging all of the above (centromeres, segmental duplications, HLA, and KIR).