Input File for Custom Annotations
The input file for custom variant annotations requires five columns: Chr, Start, Ref, Alt, and Annotation. Header rows and subannotation columns are optional. The following example shows sample entries for the columns, using the headings Tier for the annotation and Drug_Response for the subannotation.
NOTE
Annotation columns support BBCode for text formatting and linking URLs.
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##case=HDC749-Rep1 |
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##group=Tiers |
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Chr |
Start |
Ref |
Alt |
Tier |
Drug_Response |
|
2 |
209113113 |
G |
A |
Domain1 |
AG-221 | Sensitizing |
|
4 |
55599321 |
A |
T |
Domain 1 |
Imatinib | Sensitizing |
|
7 |
140453136 |
A |
T |
Domain 1 |
"Vemurafenib, Dabrafenib | Sensitizing" |
|
7 |
140453136 |
AC |
TT |
Domain 2 |
Vemurafenib | Sensitizing |
| • | Header—Instructions for case-specific annotation or default label. |
| • | Case-specific annotation—The individual case the annotation should be applied to. The header format is ##case=<case name>. |
| • | Group label—The default label for the annotation group. The header format is ##group=<group name>. |
| • | Chr—The chromosome for the variant (1–22, X, Y, or M). |
| • | Start—The genomic coordinate of the variant start position on the chromosome (1-based). |
| • | Ref—The reference base, or bases for an indel, at the specified start position. |
| • | Alt—The alternate base, or bases for an indel, at the specified start position. |
| • | Annotation—The value assigned to a variant with matching values for Chr, Start, Ref, and Alt. A pipe (|) separates multiple values. |
| • | Subannotation—The value assigned to a variant with matching values for Chr, Start, Ref, Alt, and Annotation. A pipe (|) separates multiple values. |