This vignette shows how to process long-read PacBio HiFi variant calls from a validated trio (HG002–HG003–HG004) and prepare them for UPDhmm analysis.
Ashkenazi trio (GIAB, NIST) – PacBio HiFi Revio, DeepVariant calls (GRCh38).
# Proband (HG002)
wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/PacBio_HiFi-Revio_20231031/pacbio-wgs-wdl_germline_20231031/HG002.GRCh38.deepvariant.phased.vcf.gz
wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/PacBio_HiFi-Revio_20231031/pacbio-wgs-wdl_germline_20231031/HG002.GRCh38.deepvariant.phased.vcf.gz.tbi
# Father (HG003)
wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/PacBio_HiFi-Revio_20231031/pacbio-wgs-wdl_germline_20231031/HG003.GRCh38.deepvariant.phased.vcf.gz
wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/PacBio_HiFi-Revio_20231031/pacbio-wgs-wdl_germline_20231031/HG003.GRCh38.deepvariant.phased.vcf.gz.tbi
# Mother (HG004)
wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/PacBio_HiFi-Revio_20231031/pacbio-wgs-wdl_germline_20231031/HG004.GRCh38.deepvariant.phased.vcf.gz
wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/PacBio_HiFi-Revio_20231031/pacbio-wgs-wdl_germline_20231031/HG004.GRCh38.deepvariant.phased.vcf.gz.tbi
bcftools merge \
-O z \
-o trio_HiFi_GRCh38_phased.vcf.gz \
HG002.GRCh38.deepvariant.phased.vcf.gz \
HG003.GRCh38.deepvariant.phased.vcf.gz \
HG004.GRCh38.deepvariant.phased.vcf.gz
bcftools index trio_HiFi_GRCh38_phased.vcf.gzThe following filtering steps are applied:
keep only biallelic variants
remove sites where all trio members are reference (0/0 or 0|0)
remove sites where all trio members are missing (./. or .|.)
bcftools view \
-m2 -M2 \
-e 'COUNT(GT="0/0" || GT="0|0")==3 || COUNT(GT="./." || GT=".|.")==3' \
-O z \
-o trio_HiFi_GRCh38_phased_biallelic_nonref_nomissing.vcf.gz \
trio_HiFi_GRCh38_phased.vcf.gz
bcftools index trio_HiFi_GRCh38_phased_biallelic_nonref_nomissing.vcf.gz
library(UPDhmm)
library(VariantAnnotation)
vcf <- readVcf(
"trio_HiFi_GRCh38_phased_biallelic_nonref_nomissing.vcf.gz"
)
vcf_check <- vcfCheck(
<!-- vcf, -->
proband = "HG002",
father = "HG003",
mother = "HG004"
)
events <- calculateEvents(
vcf_check,
add_ratios = TRUE
)sessionInfo()## R version 4.6.0 RC (2026-04-17 r89917)
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## other attached packages:
## [1] karyoploteR_1.38.0 regioneR_1.44.0
## [3] VariantAnnotation_1.58.0 Rsamtools_2.28.0
## [5] Biostrings_2.80.0 XVector_0.52.0
## [7] SummarizedExperiment_1.42.0 Biobase_2.72.0
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## [13] MatrixGenerics_1.24.0 matrixStats_1.5.0
## [15] BiocGenerics_0.58.0 generics_0.1.4
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