SHAPAGE hg19 Reference Repository
Year: 2026
Type: other
Abstract: SHAPAGE v1.0: REFERENCE METADATA AND DATA PROVENANCE This document details the external genomic resources integrated into the SHAPAGE pipeline. All resources are normalized to ensure cross-build compatibility. 1. REFERENCE GENOME ASSEMBLIES (FASTA) Used in Module 2 (gVCF path) for GATK Joint Genotyping and allele validation. BUILD RELEASE / SOURCE DETAILSGRCh37 GENCODE Release 37 GRCh37 mapping; primary assembly.hg19 UCSC (Feb. 2009) Original UCSC hg19 assembly. Sources:- GENCODE: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/- UCSC: https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/ 2. MEIOTIC RECOMBINATION MAPS (GENETIC MAPS)Used in Module 3 for converting physical distance (bp) to genetic distance (cM) for TMRCA estimation. BUILD (NORM) MAP TYPE METHODOLOGYhg19 / GRCh37 NCBI HapMap II Standard meiotic recombination (GRCh37). Sources: - NCBI: https://ftp.ncbi.nlm.nih.gov/hapmap/recombination/2011-01_phaseII_B37/ 3. POPULATION FREQUENCY DATABASES (GnomAD)Used in Module 2 for variant allele frequency annotation. BUILD (NORM) DATASET DESCRIPTIONhg19 / GRCh37 gnomAD v2.1.1 125,748 exomes and 15,708 genomes (GRCh37). Source: https://gnomad.broadinstitute.org/downloads To reduce storage requirements and improve processing efficiency, the gnomAD VCF files were stripped of all INFO annotations, retaining only the AF annotation required by SHAPAGE.
Author: Ventayol-Guirado, Marc
Institution: Health Research Institute of the Balearic Islands
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7170366245