VCF Test File

[alkaZeltser]

GIAB reference

This package comes with a small VCF for testing purposes. This test file is a filtered version of the NA12878/HG001 HapMap sample benchmark VCF file published by the Genome In A Bottle (GIAB) consortium (NIST v4.2.1) aligned to GRCh38.

Filter for PGS coordinates

The GIAB benchmark file contains an entire genome worth of variants, thus is too large to efficiently analyze in R and store as part of the package. It is filtered for all variant coordinates within 10bp of the PGS PGS003378, which can be accessed through the PGS catalog.

bcftools view --regions-file /path/to/PGS003378_hmPOS_GRCh38.bed -O z -o /path/to/HG001_GRCh38_1_22_v4.2.1_benchmark_in_PGS003378_hmPOS_GRCh38.vcf.gz

Addition of duplicate sample

Cohorts for polygenic scoring are typically combined into one VCF. To provide a VCF with more than one sample for testing purposes, the GIAB VCF was simply merged with itself to include a second, duplicate sample.

bcftools merge /path/to/HG001_GRCh38_1_22_v4.2.1_benchmark_in_PGS003378_hmPOS_GRCh38.vcf.gz /path/to/HG001_GRCh38_1_22_v4.2.1_benchmark_in_PGS003378_hmPOS_GRCh38.vcf.gz --force-samples -O z -o /path/to/HG001_GRCh38_1_22_v4.2.1_benchmark_in_PGS003378_hmPOS_GRCh38_duplicated-sample.vcf.gz