HPG Variant - Bioinformatics and Genomics Department at CIPF
HPG Variant - Bioinformatics and Genomics Department at CIPF HPG Variant - Bioinformatics and Genomics Department at CIPF
HPG VariantVariant Effect (I)A variant effect predictor toolPort of VARIANT tool:Queries CellBase database via a RESTful WebServices APICellBase DB: many consequence types and speciesWS, web and command-line interfaces16
HPG VariantVariant Effect (II)New back-end and command-line interfaceImplemented in C with OpenMP directivesQueries CellBase DB using libcurl libraryProcesses files of arbitrary sizeBenchmark for ~500K variants, 147 individuals:3 main threads and 4 “forked” threadsExecuted in 5:30 minutes on an Intel Xeon E31425, 8 GBRAM, network connection over Gigabit EthernetNo more than 2 GB of memory used (configurable)1500 variants per second!17
- Page 4 and 5: IntroductionData generation pipelin
- Page 7 and 8: HPC technologyOpenMPAPI for sharedm
- Page 10: HPG VCF ToolsUtilities for VCF file
- Page 14 and 15: HPG VCF ToolsHands-on demo stage 2!
- Page 18 and 19: HPG VariantGWAS Analysis (I)Genomic
- Page 20 and 21: HPG VariantGWAS Analysis (III)Comin
- Page 22 and 23: HPG VariantHands-on demo final stag
- Page 24: References1) A map of human genome
<strong>HPG</strong> <strong>Variant</strong><strong>Variant</strong> Effect (II)New back-end <strong>and</strong> comm<strong>and</strong>-line interfaceImplemented in C with OpenMP directivesQueries CellBase DB using libcurl libraryProcesses files of arbitrary sizeBenchmark for ~500K variants, 147 individuals:3 main threads <strong>and</strong> 4 “forked” threadsExecuted in 5:30 minutes on an Intel Xeon E31425, 8 GBRAM, network connection over Gigabit EthernetNo more than 2 GB of memory used (configurable)1500 variants per second!17
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