Analysis-ready BED files used for coding sequence (CDS) germline-somatic overlap analyses

Version 2 update Version 2 replaces the previously deposited HGDP rare-variant CDS BED file with the CDS subset derived from the linkage-disequilibrium-pruned rare-variant dataset used in the final analyses. The metadata were also updated to reflect the final analytical workflow. Version 1 is retained for provenance but should not be used to reproduce the final analyses. Dataset description These BED files contain autosomal biallelic single-nucleotide variants (SNVs) located within MANE-defined coding DNA sequences (CDS) in the GRCh38 human genome assembly. Variants were obtained from HGDP, ClinVar, and COSMIC source files, annotated using the Ensembl Variant Effect Predictor (VEP), and restricted to CDS intervals defined by MANE Select transcripts. Each tab-delimited BED file contains six columns: chromosome, zero-based start coordinate, end coordinate, VEP consequence, reference allele, and alternate allele. Linkage-disequilibrium pruning was applied only to the HGDP population-based datasets before restriction to CDS. File descriptions SNPs_CDS.bed.gz HGDP common SNVs. Autosomal biallelic SNVs with global allele frequency of at least 1% and allele frequency of at least 1% in two or more of the seven HGDP geographic regions, after linkage-disequilibrium pruning and restriction to MANE-defined CDS. rares_CDS.bed.gz HGDP rare SNVs. Autosomal biallelic SNVs with global allele frequency below 1%, after linkage-disequilibrium pruning and restriction to MANE-defined CDS. patho_CDS.bed.gz ClinVar SNVs classified as pathogenic or likely pathogenic and restricted to records with a review status of two to four stars, followed by restriction to MANE-defined CDS. benign_CDS.bed.gz ClinVar SNVs classified as benign or likely benign and restricted to MANE-defined CDS. cosmic_CDS.bed.gz Somatic SNVs obtained from COSMIC, deduplicated by chromosome, genomic position, reference allele, and alternate allele, and restricted to MANE-defined CDS. These analysis-ready datasets correspond to the coding-sequence inputs used to investigate exact-coordinate recurrence across germline and somatic SNV classes.