Input File for Custom Annotations
The input for custom variant annotations is a *.tsv file with the following required columns: Chr, Pos, Ref, Alt, and End. The maximum file size is 200 MB.
The following example shows sample entries for the columns, with optional columns for allele data and custom filter.
Header Rows
Header rows contain instructions for case-specific annotations. All header rows start with # and are required in the following order.
| • | Title—The label for the annotation group, which appears in the variant grid column heading. The header format is #title=<title>. |
| • | Assembly—The genome assembly, GRCh37 or GRCh38. The header format is #assembly=<assembly>. |
| • | Match variants by—The variant match option, allele or position. The header format is #matchVariantsBy=<MatchVariantsBy>. Allele frequency data only supports matching variants by allele. |
NOTE
When matching by position, multiple entries for the same variant are allowed.
| • | CHROM—The label for the chromosome annotation. If the variant exists in the VCF being annotated, the label and associated value are listed in the variant details tab. |
| • | Categories—The custom annotation category, which indicates the type of data represented in the column. Predefined fields (Chrom, Pos, Ref, and Alt) do not require a category. |
| • | AlleleCount—Allele counts for a specific population. |
| • | AlleleFrequency —Allele frequencies for a specific population. |
| • | AlleleNumber—Total number of alleles for a specific population. |
| • | Filter—Free text field to create a custom label up to 20 characters in length. |
| • | Descriptions—Additional text to describe data related to the variant. This field is not sortable or filterable. In the example input file, the description field is used to indicate that the allele frequencies apply for all populations. |
| • | Type—The input type, which can be number or string. |
Annotation Details
The first five columns (Chr, Pos, Ref, Alt, and End) are required in the order listed.
| • | Chr—The chromosome for the variant (1–22, X, Y, or M). |
| • | Pos—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. Required for small variants. For other variant types, enter a period in this field. |
| • | Alt—The alternate base, or bases for an indel, at the specified start position. Required for small variants. For other variant types, enter a period in this field. |
| • | End—The genomic coordinate of the large variant end position. For small variants, enter a period in this field. |
| • | Annotation—The value assigned to a variant with matching values for Chr, Pos, Ref, and Alt. |
| • | Subannotation—The value assigned to a variant with matching values for Chr, Start, Ref, Alt, and Annotation. A pipe (|) separates multiple values. |
Example
NOTE
Annotation columns support BBCode for text formatting and linking URLs.
#title=InternalAnnotation
#assembly=GRCh37
#matchVariantsBy=allele
#CHROM POS REF ALT END allAf customLabel
#categories . . . . AlleleFrequency Filter
#descriptions . . . . ALL .
#type . . . . number string
chr1 11856378 G A . 0.00016 FP
chr2 210640622 C T . 0.0003 FP
chr5 1216900 G A . 0.001 CV
chr7 150696111 T G . 0.001 BL
chr8 11614575 A G . 0.01 BL
chr19 13010521 G A . 0.02 CV