CNV manual import format

This page describes the manual import format for CNV variants into ELLA anno.

• VCF Glossary
• Generalized format
  • Deletions
  • Tandem Duplications
  • Duplications with unknown copy location
• Examples with VCF type, CN and GT
  • Autosomal
  • X chromosome
  • Y chromosome

VCF Glossary

• CN: estimated total copy number in the sample
• GT: genotype, encoding alleles as numbers (0 for the reference allele)

Generalized format

Deletions

VCF

This correponds to the <DEL> VCF type. CN and GT can be inferred.

<chr>:<start>_<stop>del [het|hom]

Example: 
3:1234_1345del hom

Tandem Duplications

VCF

This correponds to the <DUP:TANDEM> VCF type. CN and GT can be inferred.

<chr>:<start>_<stop>dup [het|hom]

Example: 
3:1234_1345dup het

NOTE

By HGVS definition (opens new window), "dup" should only be used for tandem duplications, i.e., where the additional copy is directly 3'-flanking of the original copy.

For all other cases, including when the copy location is unknown, use the format below.

Duplications with unknown copy location

VCF

This correponds to the <DUP> VCF type. CN is the same as #, but GT cannot be inferred.

<chr>:<start>_<stop> x<#>

Example:
3:1234_1345 x3

NOTE

On X and Y chromosomes, # (CN) = 2 should be allowed (on X, for males only), but not on autosomes.

Examples with VCF type, CN and GT

Autosomal

Type	Core	Example import	VCF type	VCF CN	VCF GT
Del (hom)	<chr>:<start>_<stop>del hom	3:1234_1345del hom	<DEL>	0	1/1
Del (het)	<chr>:<start>_<stop>del het	3:1234_1345del het	<DEL>	1	0/1
Tandem Dup (het)	<chr>:<start>_<stop>dup het	3:1234_1345dup het	<DUP:TANDEM>	3	0/1
Tandem Dup (hom)	<chr>:<start>_<stop>dup hom	3:1234_1345dup hom	<DUP:TANDEM>	4	1/1
Copy number 3	<chr>:<start>_<stop> x3	3:1234_1345 x3	<DUP>	3	./.
Copy number 4	<chr>:<start>_<stop> x4	3:1234_1345 x4	<DUP>	4	./.

X chromosome

Type	Core	Example import	VCF type	VCF CN	VCF GT
Del (hemi/hom)	X:<start>_<stop>del hom	X:1234_1345del hom	<DEL>	0	1[/1]
Del (het)	X:<start>_<stop>del het	X:1234_1345del het	<DEL>	1	0/1
Tandem Dup (het)	X:<start>_<stop>dup het	X:1234_1345dup het	<DUP:TANDEM>	3	0/1
Tandem Dup (hemi/hom)	X:<start>_<stop>dup hom	X:1234_1345dup hom	<DUP:TANDEM>	2/4	1[/1]
Copy number 2	X:<start>_<stop> x2	X:1234_1345 x2	<DUP>	2	./.
Copy number 3	X:<start>_<stop> x3	X:1234_1345 x3	<DUP>	3	./.
Copy number 4	X:<start>_<stop> x4	X:1234_1345 x4	<DUP>	4	./.

Y chromosome

Type	Core	Example import	VCF type	VCF CN	VCF GT
Del (hemi)	Y:<start>_<stop>del	Y:1234_1345del	<DEL>	0	1
Tandem Dup	Y:<start>_<stop>dup	Y:1234_1345dup	<DUP:TANDEM>	2	1
Copy number 2	Y:<start>_<stop> x2	Y:1234_1345 x2	<DUP>	2	.