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The variant calling pipeline processes the deduped and recalibrated BAMs file produced by the alignment pipeline or that you provide it, generating an initial list of polymorphic sites and genotypes stored in a [http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 VCF (Variant Call Format) file]. The variant calling pipeline then filters the variants using both hard filters and a [[SVM Filtering|Support Vector Machine (SVM)]]. It then uses haplotype information to refine these genotypes in an updated VCF file.
The variant calling pipeline processes the deduped and recalibrated BAMs file produced by the alignment pipeline or that you provide it, generating an initial list of polymorphic sites and genotypes stored in a [http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 VCF (Variant Call Format) file]. The variant calling pipeline then filters the variants using both hard filters and a [[SVM Filtering|Support Vector Machine (SVM)]]. It then uses haplotype information to refine these genotypes in an updated VCF file.
After completing the GotCloud Variant Calling PIpeline, [[EPACTS|EPACTS (Efficient and Parallelizable Association Container Toolbox)]] can be used to perform statistical tests to identify genome-wide association from sequence data.
After completing the GotCloud Variant Calling Pipeline, [[EPACTS|EPACTS (Efficient and Parallelizable Association Container Toolbox)]] can be used to perform statistical tests to identify genome-wide association from sequence data.
[[File:GotCloudDiagram.jpg|500px]]
[[File:GotCloudDiagram.jpg|500px]]
