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 4.6.1 (2026-06-24)
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## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
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## other attached packages:
## [1] karyoploteR_1.39.0 regioneR_1.45.2
## [3] VariantAnnotation_1.59.4 Rsamtools_2.29.0
## [5] Biostrings_2.81.9 XVector_0.53.0
## [7] SummarizedExperiment_1.43.0 Biobase_2.73.2
## [9] GenomicRanges_1.65.4 IRanges_2.47.5
## [11] S4Vectors_0.51.10 Seqinfo_1.3.2
## [13] MatrixGenerics_1.25.0 matrixStats_1.5.0
## [15] BiocGenerics_0.59.12 generics_0.1.4
## [17] dplyr_1.2.1 UPDhmm_1.9.1
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## [70] lazyeval_0.2.3 Hmisc_5.3-0 tools_4.6.1
## [73] BiocIO_1.23.3 data.table_1.18.6.1 BSgenome_1.81.1
## [76] GenomicAlignments_1.49.2 XML_3.99-0.25 grid_4.6.1
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