STR Annotation Threshold Files
The input for custom STR annotation thresholds is a *.tsv file that specifies the number of units required for annotation of repeat expansions in the specified genome build.
STR annotation threshold files contain a header section and a data section:
| • | Header—The header row specifies the genome assembly, GRCh37 or GRCh38, in the format #assembly=<assembly>. |
| • | Data—The data section includes columns described in the following table. Each row corresponds to a loci. |
|
Field |
Description |
|---|---|
|
Chrom |
The name of the chromosome. |
|
Start |
The genomic coordinate of the start position. |
|
End |
The genomic coordinate of the end position. |
|
Phenotype |
The phenotype associated with the STR. |
|
OMIM ID |
The OMIM ID for the phenotype. |
|
Repeat numbers |
The observed repeat lengths. |
|
Allele counts |
The number of times a repeat length has been observed, listed in order by repeat number. |
|
Classifications |
The STR classification. Possible entries are Normal and Expanded. |
|
Classification ranges |
The thresholds for normal and expanded classifications. Modify the ranges to change the genetic finding classifications. |
Example
|
#assembly=GRCh37 |
|
|
||||||
|
#Chrom |
Start |
End |
Phenotype |
OMIM_ID |
Repeat_numbers |
Allele_counts |
Classifications |
Classification_range |
|
chr19 |
13207859 |
13207897 |
Spinocerebellar ataxia 6 |
183086 |
4,7,8,10,11,12,13,14,15,38 |
2,28,1,4,102,62,85,13,2,1 |
Normal, Expanded |
0-18, 19-inf |
|
chr22 |
4579535 |
45795424 |
Spinocerebellar ataxia 10 |
603516 |
7,9,11,12,13,14,15,16,17,18,19 |
2,1,7,43,75,87,43,21,11,6,4 |
Normal, Expanded |
0-32,33-inf |
