Variant IDs

Overview

Many downstream tools use a variant identifier to store annotation results.

Deprecated

This initial variant ID (VID) scheme was designed to be parsimonious and was not meant to be used to reconstitute the original VCF variant. In later versions of Nirvana, we migrated to the identifier scheme used at the Broad Institute (with some extensions to handle structural variants).

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

SNV

VCF Example

chr1    69224   .   A   C   .   .   .

Format

chromosome:position:alternate allele

VID Example

• 1:69224:C

Insertion

VCF Example

chr1    69567   .   A   AT  .   .   .

Format

chromosome:position after insertion:position before insertion:alternate allele OR MD5 hash

If more than 32 bases are being inserted, the VID scheme uses an MD5 checksum instead

VID Example

• 1:69568:69567:T
• 1:69568:69567:B9ECE18C950AFBFA6B0FDBFA4FF731D3

Deletion

VCF Example

chr1    136647  .   GG  G   .   .   .

Format

chromosome:start position:end position

VID Example

• 1:136645:136645

Delins

VCF Example

chr1    965025  .   GCAGTGCATGGTGCTGTGAGATCAGCATGTGTG   GTGCAGTGCATGGTGCTGTGAGATCAGCA   .   .   .

Format

chromosome:start position:end position:inserted bases

If more than 32 bases are being inserted, the VID scheme uses an MD5 checksum instead

VID Example

• 1:965026:965057:TGCAGTGCATGGTGCTGTGAGATCAGCA
• 1:965026:965057:5DC27E17BE0B0F184325DC8654E34F1F

MNV

VCF Example

chr1    979210  .   TGG TTT .   .   .

Format

chromosome:start position:end position:alternate allele

If more than 32 bases are being inserted, the VID scheme uses an MD5 checksum instead

VID Example

• 1:979211:979212:TT
• 1:979211:979212:DF1F3EDB9115ACB0A1E04209B7A9937B

CNV

VCF Example

chr1    854895  .   N   <CN0>,<CN3> .   PASS    SVTYPE=CNV;END=861879;CNVLEN=6984;CIPOS=-291,291;CIEND=-291,291 GT:RC:BC:CN:MCC:MCCQ:QS:FT:DQ   1/2:165.40:12:3:3:16.80:16.71:PASS:.
chr1    814866  .   N   <CNV>   4   q10;CLT10kb SVTYPE=CNV;END=824517   RC:BC:CN    214:7:4

Format

chromosome:start position:end position:copy number or "CNV"

VID Example

• 1:854896:861879:3
• 1:814867:824517:CNV

Inversion (SV)

VCF Example

chr1    17051724    .   C   <INV>   3070    MaxDepth    END=234912187;SVTYPE=INV;SVLEN=217860463    GT:GQ:PR:SR 0/1:3070:77,69:84,76

Format

chromosome:start position:end position:Inverse

VID Example

• 1:17051725:234912187:Inverse

Translocation (SV)

VCF Example

chr1    797265  .   G   G]chr8:245687]  55  PASS    SVTYPE=BND;CIPOS=0,31   GT:GQ:PR:SR 0/1:55:39,6:20,3

Format

chromosome 1:breakpoint 1:orientation 1:chromosome 2:breakpoint 2:orientation 2

VID Example

• 1:797265:+:8:245687:-

Deletion (SV)

VCF Example

chr1    2053194 .   G   <DEL>   38  PASS    END=2055480;SVTYPE=DEL;SVLEN=-2286;IMPRECISE;CIPOS=-143,144;CIEND=-102,102  GT:GQ:PR    0/1:38:3,5

Format

chromosome:start position:end position

VID Example

• 1:2053195:2055480

Insertion (SV)

VCF Example

chr1    1925144 .   G   <INS>   1439    PASS    END=1925144;SVTYPE=INS;CIPOS=0,14;CIEND=0,14    GT:GQ:PR:SR 1/1:72:2,7:0,33

Format

chromosome:start position:end position:INS

VID Example

• 1:1925145:1925144:INS

Tandem Duplication (SV)

VCF Example

chr1    2454149 .   G   <DUP:TANDEM>    976 MaxDepth    END=2454244;SVTYPE=DUP;SVLEN=95;CIPOS=0,10;CIEND=0,10   GT:GQ:PR:SR 0/1:976:6,0:80,52

Format

chromosome:start position:end position:TDUP

VID Example

• 1:2454150:2454244:TDUP