ABOUT


The TIGEM Exome Mendelian Disorder Tool is a resource to annotate and analyze whole exome-sequencing data from patients. The underlying pipeline automates the analysis workflow (quality control and read trimming, mapping on reference genome, post-alignment processing, variation calling and annotation) using state-of-the-art software tools. The results are annotated with allele frequencies stratified by Mendelian disorder calculated by the samples progressively collected in the database, as long as the standard variant annotation (e.g. allele frequency in the general population, the predicted effect on gene product activity, etc.).



Publications

Mutarelli M, Marwah VS, Rispoli R, Carrella D, Dharmalingam G, Oliva G and di Bernardo D.
A community-based resource for automatic exome variant-calling and annotation in Mendelian disorders.
BMC Genomics 2014, 15(Suppl 3):S5 (6 May 2014). Abstract



Diseases Table

NameSamples Number
Orofaciodigital Syndromes; MESH:D00995819
Limb-girdle muscular dystrophy autosomal recessive; MESH:C53864014
Usher Syndromes; MESH:D052245; OMIM:5000049
Microphthalmia, syndromic 7; MESH:C537466; OMIM:3098018
Retinitis Pigmentosa; MESH:D012174; OMIM:268000,OMIM:300155,OMIM:300424,OMIM:602594,OMIM:6060686
Nephritis, Hereditary; MESH:D0093945
Prognathism; MESH:D0113785
Muscular Dystrophy, Limb-Girdle, Type 1F; MESH:C564242; OMIM:6084234
Distal Myopathies; MESH:D049310; OMIM:160500,OMIM:606070,OMIM:6100993
Microphthalmos; MESH:D0088502
Orofaciodigital syndrome type1; MESH:C537134; OMIM:3112001


Analysis Tools

NameVersionProcesses
FASTQC0.10.1Sequence QC
Trim Galore0.3.1Sequence Trimming
BEDtools2.16.2Coverage Statistics
BWA0.6.2Sequence Alignment
SAMtools0.1.19Alignment Statistics
Picard1.81MarkDuplicates
GATK2.7-4IndelRealigner
BaseRecalibrator
UnifiedGenotyper
Annovar2013May20Annotate Variations



For any information please contact exome-support@tigem.it