Bcftools norm command line wrapper.
Bcftools norm command line arguments.
Bcftools norm wrapper as a function VariantContextRDD → VariantContextRDD, for use in cannoli-shell or notebooks.
Bcftools norm function arguments.
Bedtools intersect command line wrapper.
Bedtools intersect command line arguments.
Bedtools intersect wrapper as a function FeatureRDD → FeatureRDD, for use in cannoli-shell or notebooks.
Bedtools intersect function arguments.
Bowtie command line wrapper.
Bowtie 2 command line wrapper.
Bowtie 2 command line arguments.
Bowtie 2 wrapper as a function FragmentRDD → AlignmentRecordRDD, for use in cannoli-shell or notebooks.
Bowtie 2 function arguments.
Bowtie command line arguments.
Bowtie wrapper as a function FragmentRDD → AlignmentRecordRDD, for use in cannoli-shell or notebooks.
Bowtie function arguments.
Bwa command line wrapper.
Bwa command line arguments.
Bwa wrapper as a function FragmentRDD → AlignmentRecordRDD, for use in cannoli-shell or notebooks.
Bwa function arguments.
Cannoli main.
Cannoli function.
Cannoli function.
Cannoli function argument type parameter.
Cannoli function result type parameter.
Cannoli module, binds the default list of command groups.
Freebayes command line wrapper.
Freebayes command line arguments.
Freebayes wrapper as a function AlignmentRecordRDD → VariantContextRDD, for use in cannoli-shell or notebooks.
Freebayes function arguments.
Interleaves two FASTQ files.
Sample reads from interleaved FASTQ format.
Samtools mpileup command line wrapper.
Samtools mpileup command line arguments.
Samtools mpileup wrapper as a function AlignmentRecordRDD → VariantContextRDD, for use in cannoli-shell or notebooks.
Samtools mpileup function arguments.
SnpEff command line wrapper.
SnpEff command line arguments.
SnpEff wrapper as a function VariantContextRDD → VariantContextRDD, for use in cannoli-shell or notebooks.
SnpEff function arguments.
Vt normalize command line wrapper.
Vt normalize command line arguments.
Vt normalize wrapper as a function VariantContextRDD → VariantContextRDD, for use in cannoli-shell or notebooks.
Vt normalize function arguments.
Bedtools intersect wrapper as a function FeatureRDD → FeatureRDD, 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)