Annotate genes from list¶
The Annotate genes from list report builder cross-references variants in a gorreport (containing chromosome, position, reference, and call columns) with a defined gene list. The output displays the original variant GOR report with an additional column called the InGeneList column (which indicates “yes” or “no” membership in the defined gene list).
Annotate Genes From List in Sequence Miner¶
Example use case¶
This module allows the user to quickly compare a variant report with a list of genes to determine whether the variants are in the target gene list or not.
To use the module, the user must first have two tabs open with the following information:
A GOR report consisting of a list of variants of interest with genomic coordinates;
A reference list of gene symbols of interest (defined gene list).
In this case, the user wishes to find out if any of the variants in the GOR report affect any gene(s) in the defined gene list. The gene list must only contain a list of genes. Therefore, all other columns must be hidden using the column filters in that tab.
The Gene List must contain only one column with gene_symbols¶
It is also necessary to indicate if there is a gene_symbol column in the variant GOR report. If there is a gene_symbol column in the variant GOR report, the module will determine if the gene_symbol listed in the variant GOR report is in the defined genelist. Otherwise, the module will perform a -snpseg join with a fuzz factor of 10 to the genes table and add the InGeneList column with the appropriate values.
Description of the algorithm¶
This dialog searches the variant GOR report for genes that are in the defined genelist for genes. An InGeneList column is added to the variant GOR report to indicate (“yes” or “no”) presence or absence in the defined gene list.
Interpreting of the output¶
The InGeneList column entry (“yes” or “no”) indicates the presence or absence of the variant gene in the genelist.
Column descriptions¶
Group |
Column |
Description |
|---|---|---|
Basic |
Call |
|
Chrom |
||
POS |
||
Reference |
||
Other columns |
InGeneList |
“yes” or “no” indicates presence or absence of the variant gene in the genelist |