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Quick Start

Small variants (MAF → flanks)

vflank small run variants.maf \
    --ref-genome GRCh37.fasta \
    --genome-build hg19 \
    --flank 200 \
    --output flanking_sequences.fasta

Each unique variant yields two FASTA records — raw and masked:

>{GENE}__{HGVSp}__{HGVSc}__{CHROM}_{POS}_{REF}_{ALT}
{left_flank}[REF/ALT]{right_flank}
>Masked__{GENE}__{HGVSp}__{HGVSc}__{CHROM}_{POS}_{REF}_{ALT}
{left_flank_masked}[REF/ALT]{right_flank_masked}

Add SNP masking with no download via the gnomAD API:

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

Or skip the local FASTA too — fetch the reference from the UCSC API with --ref-source api (then --ref-genome is not needed):

vflank small run variants.maf -g hg19 --ref-source api --pop-source api

Preview your MAF first

vflank small inspect variants.maf shows the columns and flags missing required fields before a full run.

Fusions (breakpoint table → junctions)

Input is a tab-separated breakpoint table — columns matched by name:

chr1    pos1    str1    chr2    pos2    str2    name
22  29684066    0   11  32416521    1   EWSR1-WT1

(str: 0 = plus/reference, 1 = minus/complement, matching iCallSV.)

vflank fusion run breakpoints.tsv \
    --ref-genome GRCh37.fasta \
    --genome-build hg19 \
    --flank 200 \
    --output fusion_junctions.fasta

Each fusion yields the junction sequence (raw + masked), with the probe designed to span the join.

Next steps