SNP Masking

Common germline SNPs under a primer or probe cause allele dropout and assay failure. vflank masks them to N in the Masked__ records so a downstream designer avoids those positions. Both small and fusion share the same options.

Two backends — --pop-source

Local VCFs (default)gnomAD API (no download)

vflank small run variants.maf -r GRCh37.fasta -g hg19 \
    --pop-source vcf --pop-vcf-dir gnomad_v2.1.1/

Reproducible, offline, unlimited scale. Verify coverage first:

vflank small list-vcf gnomad_v2.1.1/ -g hg19 --pop-data both

vflank small run variants.maf -r GRCh37.fasta -g hg19 --pop-source api

Queries https://gnomad.broadinstitute.org/api per flank region — no data to download. Rate-limited to ~10 requests/min, so best for small cohorts; identical variants are cached to one request.

	Local VCF	gnomAD API
Setup	download per-chromosome VCFs	none
Reproducible / offline	✅	❌ (network; data updates)
Scale	unlimited	small cohorts (rate limit)

Which data — --pop-data {genome,exome,both}

Default genome. Flanks often fall in non-coding regions where only genomes have data; exome adds power in coding regions; both masks the union (a position is masked if it is a common SNP in either cohort).

A position is masked when a single-base gnomAD SNP there has max(AF, AF_grpmax) ≥ --af-threshold (default 0.001 = 0.1%). Indels are not masked. Requesting exome/both from the VCF backend without the exome files fails fast — never a silent genome-only fallback.

Genome builds

--genome-build	Reference	gnomAD
hg19 (default)	GRCh37	v2.1.1
hg38	GRCh38	v4.1

gnomAD v4 is GRCh38-only — there is no v4 GRCh37.

Downloading gnomAD VCFs (GRCh37 example)

mkdir -p gnomad_v2.1.1 && cd gnomad_v2.1.1
BASE=https://storage.googleapis.com/gcp-public-data--gnomad/release/2.1.1/vcf/genomes
for CHR in {1..22} X; do
  wget -c "$BASE/gnomad.genomes.r2.1.1.sites.${CHR}.vcf.bgz"
  wget -c "$BASE/gnomad.genomes.r2.1.1.sites.${CHR}.vcf.bgz.tbi"
done

Exome files use gnomad.exomes.* (needed only for --pop-data exome/both). Download only the chromosomes your variants are on to save space.