I am writing out tandem repeat variation to VCF format and I would like to use the best possible identifier.
From VCF 4.1, docs state:
"The ID field indicates the type of structural variant, and can be a colon-separated list of types and subtypes. ID values are case sensitive strings and may not contain whitespace or angle brackets. The first level type must be one of the following:
DEL Deletion relative to the reference
INS Insertion of novel sequence relative to the reference
DUP Region of elevated copy number relative to the reference
INV Inversion of reference sequence
CNV Copy number variable region (may be both deletion and duplication)
The CNV category should not be used when a more specific category can be applied. Reserved subtypes include:
DUP:TANDEM Tandem duplication
DEL:ME Deletion of mobile element relative to the reference
INS:ME Insertion of a mobile element relative to the reference"
Certainly if we have a repeat like TATATA, mutations could be described as INS or DEL but I think there should be separate identifier for tandem repeats.
Thoughts?
From VCF 4.1, docs state:
"The ID field indicates the type of structural variant, and can be a colon-separated list of types and subtypes. ID values are case sensitive strings and may not contain whitespace or angle brackets. The first level type must be one of the following:
DEL Deletion relative to the reference
INS Insertion of novel sequence relative to the reference
DUP Region of elevated copy number relative to the reference
INV Inversion of reference sequence
CNV Copy number variable region (may be both deletion and duplication)
The CNV category should not be used when a more specific category can be applied. Reserved subtypes include:
DUP:TANDEM Tandem duplication
DEL:ME Deletion of mobile element relative to the reference
INS:ME Insertion of a mobile element relative to the reference"
Certainly if we have a repeat like TATATA, mutations could be described as INS or DEL but I think there should be separate identifier for tandem repeats.
Thoughts?