1. In the Step1:Upload Samples and Assign Parameters process (Try to analysis), users have to upload vcf files to continue analysis.
2. Linkage regions in Physical coordinates format and Genetic coordinates format are provided (See example), users can perform further steps of customized analysis.
PedMiner offers two demo pedigree files (vcfs & pedigree chart) together with the whole analysis process,users can learn from the demos on how to assign parameters properly to run the analysis process and how to analysis the output results (View detail).
Sample-naming errors or confusions are occasionally arising in family-based DNA sequencing studies. To avoid the resulting error analysis, PedMiner integrates a relationship inference function to check the relationship among family members.
PedMiner offers a default filtration process to prioritize the candidate variants. Users can further filter candidates via web page directly by setting the threshold for each annotation item.
In case of the candidate pathogenic variants were not directly found in the exome area of the linkage region, in addition, PedMiner provides annotation for all genes in the region, so that the user can select candidate pathogenic genes based on the known functions of the gene.
The annotaion information including linkage region, variant site, variant consequence, MAF, noxiousness prediction by multiple tools, corresponding gene and orthologous in mice.
PedMiner can perform linkage analysis directly using family-based WES data.
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