Reports is an interactive graphical interface designed to facilitate data analysis and is based on the GOR language. The Reports tab opens by default when the Sequence Miner application is opened from the Clinical Sequence Analyzer (CSA) dashboard, displaying a grid which lists all available report modules.
To open any one of the modules in Sequence Miner, click on the module in the grid. The grid can be sorted according to the category/type of module.
Using Report Builders¶
The Reports tab contains a set of predefined report modules, also known as report builders, which can be used to parameterize a variety of different types of reports. There are over forty different modules currently available which target variant and gene annotation, Mendelian inheritance analysis, and cohort analysis use cases.
The Reports tab displays all available report builders as tiles. Clicking on a tile opens the selected report builder in a new tab, where input parameters can be edited to run the report.
Filtering and search¶
Report builders can be filtered by report type by clicking the arrow to open the drop-down menu. You can also search for individual report builders by entering keywords into the search bar, which searches report builder names, parameter names, and text descriptions.
To save a report builder to your favorites, toggle the star icon in the upper right-hand corner of the selected report builder tile. To show only your favorite report builders, toggle the star icon next to the search bar.
Reordering and undocking tabs¶
To reorder open tabs in the Sequence Miner window, click on a tab and drag it to a new location.
To undock a tab from the window, by right-click on the tab title and select Undock. To redock the tab into Sequence Miner, close the undocked window.
Tabs can be renamed by right-clicking the tab title and selecting Set Title.
In the Set title dialog, enter a new title and click OK. Tab titles can include alphanumeric and underscore characters only.
When you have completed the form associated with any report, the Create Report button changes color from grey to light blue, indicating that you have entered sufficient input arguments to run the report. Click the button to generate the report.
The table below shows a list of the available report builders in Sequence Miner in the Cancer category with a short description of each. Note that Cancer modules are included only in selected installations of Sequence Miner and that your setup may be different.
|Cancer QC and statistics||Calculates and reports variant statistics for tumor samples|
|CNV analyzer||Annotates and summarizes copy number variation (CNV) calls from the CNVkit caller for tumor samples|
|Differential expression analysis using edgeR||Determine differentially expressed genes between two or more groups of samples|
|Gene association cancer||Gene-aggregated variant analysis|
|Methylation summary||Provides the methylation status of samples at the individual probe level, gene level, or transcript level|
|mRNA summary||Provides expression sequencing data information for samples|
|miRNA summary||Provides miRNA expression sequencing data information for samples|
|Mutational signatures||Count variants per VEP category|
|Sample map - TCGA||Map samples across different data types available in the TCGA multi-omic dataset|
|Tumor mutation analysis||Counts the number of heterozygous, homozygous, and compound heterozygous variants in case and control subjects that pass filtering parameters|
|Tumor mutation burden||Generate input table for statistical tools|
The table below shows a list of the available report builders in Sequence Miner in the Case/Control category with a short description of each.
|Gene analysis||Count variants and variants in gene for a cohort|
|Gene association||Gene-aggregated variant analysis|
|Gene count||Count variants per VEP category|
|Phenogrid||Generate input table for statistical tools|
|Recessive analysis||Counts the number of heterozygous, homozygous, and compound heterozygous variants in case and control subjects that pass filtering parameters|
|Sequence Kernel Association Test (SKAT)||Evaluate the effect of variants on continuous or dichotomous traits using the sequence kernel association test (SKAT).|
|Single point regression||Apply linear or logistic regression to quantify the relationship between specified variants and phenotypic data|
|Variant association||Single variant case-control association using Fisher Exact|
|Variant association ExAC (WES)||Single variant case-control association using Fisher Exact for multiplactive (mm), recessive (rc), and dominant (dc) genetic models, using the Exome Aggregation Consortium (ExAC) database as controls.|
|Variant count||Count variants in a cohort|
The table below shows a list of the available report builders in Sequence Miner in the Gene category with a short description of each.
|Annotate genes from list||Cross-reference a report with a gene list|
|Gene carrier report||Find carriers of variants in a genelist|
|Gene ontology association||Quantify the association between a list of genes and categories in the Gene Ontology (GO) database|
|Gene ontology to genes||Gene associated with Gene Ontology (GO) codes|
|Gene/protein ID converter||Maps/converts gene and protein IDs from reference source to all others and provide gene/protein names and IDs in a set of user-provided genomic regions|
|Genes to paralogs||Generate a report listing all paralogs of genes in a list|
|Genes to pathways||Maps list of genes to corresponding pathway(s)|
|Paralog disease annotation||Annotate variants with the disease(s) associated with genes and their paralogs|
|Pathways to genes||Maps selected pathway(s) to a set of related genes in the same pathway(s)|
The table below shows a list of the available report builders in Sequence Miner in the Inheritance category with a short description of each.
|Carrier||Preconception disease gene carrier analysis for parents|
|De novo/CHZ for trios||Trio de novo variant analysis and annotation|
|Mendelian analysis||Single index case Mendelian disease analysis|
|Multi-family Mendelian analysis||Zygosity analysis for cases versus controls|
Quality Control (QC)¶
The table below shows a list of the available report builders in Sequence Miner in the Quality Control (QC) category with a short description of each.
|Exon coverage||Calculate the exon coverage for one or more subjects using Ensembl transcripts|
|Gene coverage||Calculate the gene coverage for one or more subjects|
|Sample QC and statistics||Calculate quality statistics for multiple subjects|
|Sex check||Check the sex of the samples|
|Sharing||Calculate the kinship of individuals|
|Variant QC and statistics||Generate a variant summary for subject(s)|
The table below shows a list of the available report builders in Sequence Miner in the Search category with short description of each.
|Sample search||Identify subjects with information that matches the input keywords|
The table below shows a list of the available report builders in Sequence Miner in the Variant category with a short description of each.
|Annotate variants||Annotate variants in selected genes|
|Annotate variants from file||Annotate variants with your own file|
|Compare GOR reports||Compare two reports|
|Liftover||Convert the genomic positions from one genome build to another|
|Loss of heterozygosity||Identify regions of loss of heterozygosity|
|Overlapping variants||Count the variants within a gene list|
|Risk SNPs||Return SNP genotypes for rsIDs|
|Transcripts||Variant transcript effect|
|Venn variant analysis||Compare variant reports with Venn visualization|