Bcftools mpileup wrapper as a function AlignmentRecordDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
Bcftools mpileup function arguments.
Bcftools norm wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
Bcftools norm function arguments.
Bedtools intersect wrapper as a function FeatureDataset → FeatureDataset, for use in cannoli-shell or notebooks.
Bedtools intersect function arguments.
Bowtie wrapper as a function FragmentDataset → AlignmentRecordDataset, for use in cannoli-shell or notebooks.
Bowtie 2 wrapper as a function FragmentDataset → AlignmentRecordDataset, for use in cannoli-shell or notebooks.
Bowtie 2 function arguments.
Bowtie function arguments.
Bwa wrapper as a function FragmentDataset → AlignmentRecordDataset, for use in cannoli-shell or notebooks.
Bwa function arguments.
Cannoli function.
Cannoli function.
Cannoli function argument type parameter.
Cannoli function result type parameter.
Freebayes wrapper as a function AlignmentRecordDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
Freebayes function arguments.
GEM-Mapper wrapper as a function FragmentDataset → AlignmentRecordDataset, for use in cannoli-shell or notebooks.
GEM-Mapper function arguments.
Minimap2 wrapper as a function FragmentDataset → AlignmentRecordDataset, for use in cannoli-shell or notebooks.
Minimap2 function arguments.
Samtools mpileup wrapper as a function AlignmentRecordDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
Samtools mpileup function arguments.
SnpEff wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
SnpEff function arguments.
Vep wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
Vep function arguments.
Vt normalize wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
Vt normalize function arguments.
Bedtools intersect wrapper as a function FeatureDataset → FeatureDataset, for use in cannoli-shell or notebooks.
val args = new BedtoolsIntersectFnArgs() args.b = "foo.bed" args.useDocker = true val features = ... val pipedFeatures = new BedtoolsIntersectFn(args, sc).apply(features)