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Version: 3.14

Variant IDs

Overview

Many downstream tools use a variant identifier to store annotation results. We've standardized on using variant identifiers (VIDs) that originated from the notation used by the Broad Institute.

The Broad VID scheme is not only simple, but it has the advantage that a user could create a bare bones VCF entry from the information captured in the identifier. One of the limitations of the Broad VID scheme is that it does not define how to handle structural variants. Our VID scheme attempts to fill that gap.

Conventions
  • all chromosomes use Ensembl style notation (i.e. 22 instead of chr22)
  • for a reference variant (i.e. no alt allele), replace the period (.) with the reference base
  • padding bases are used, neither the reference nor alternate allele can be empty
  • some large variant callers lazily output N for the reference allele. If this is the case, replace it with the true reference base

Small Variants

VCF Examples

chr1    66507   .   T   A   184.45  PASS    .
chr1    66521   .   T   TATATA  144.53  PASS    .
chr1    66572   .   GTA G,GTACTATATATTATA   45.45   PASS    .

Format

chromosome—position—reference allele—alternate allele

VID Examples

  • 1-66507-T-A
  • 1-66521-T-TATATA
  • 1-66572-GTA-G
  • 1-66572-G-GTACTATATATTA

Translocation Breakends

VCF Example

chr1    2617277 .   A   AAAAAAAAAAAAAAAAAATTAGTCAGGCAC[chr3:153444911[  .   PASS    SVTYPE=BND

Format

chromosome—position—reference allele—alternate allele

VID Example

  • 1-2617277-A-AAAAAAAAAAAAAAAAAATTAGTCAGGCAC[chr3:153444911[

All Other Structural Variants

VCF Examples

chr1    1000    .   G   <ROH>   .   PASS    END=3001000;SVTYPE=ROH
chr1    1350082 .   G   <DEL>   .   PASS    END=1351320;SVTYPE=DEL
chr1    1477854 .   C   <DUP:TANDEM>    .   PASS    END=1477984;SVTYPE=DUP
chr1    1477968 .   T   <INS>   .   PASS    END=1477968;SVTYPE=INS
chr1    1715898 .   N   <DUP>   .   PASS    SVTYPE=CNV;END=1750149
chr1    2650426 .   N   <DEL>   .   PASS    SVTYPE=CNV;END=2653074
chr2    321682  .   T   <INV>   .   PASS    SVTYPE=INV;END=421681
chr20   2633403 .   G   <STR2>  .   PASS    END=2633421

Format

chromosome—position—end position—reference allele—alternate allele—SVTYPE

VID Examples

  • 1-1000-3001000-G-<ROH>-ROH
  • 1-1350082-1351320-G-<DEL>-DEL
  • 1-1477854-1477984-C-<DUP:TANDEM>-DUP
  • 1-1477968-1477968-T-<INS>-INS
  • 1-1715898-1750149-A-<DUP>-CNV (replace the N with A)
  • 1-2650426-2653074-N-<DEL>-CNV (keep the N)
  • 2-321682-421681-T-<INV>-INV
  • 20-2633403-2633421-G-<STR2>-STR