pipelines

Type Members

1. class CreateUnmappedBamFromFastqPipeline extends Pipeline

   

   Annotations

   @ClpAnnotation()

2. class DnaResequencingFromFastqPipeline extends Pipeline

   

   Annotations

   @ClpAnnotation()

3. class DnaResequencingFromUnmappedBamPipeline extends Pipeline

   

   Annotations

   @ClpAnnotation()

4. class DownsampleAndCallSomaticVariants extends Pipeline

   

   Pipeline to downsample a Tumor to a specific median coverage level (per CollectHsMetrics) and run somatic variant calling on it.

   Pipeline to downsample a Tumor to a specific median coverage level (per CollectHsMetrics) and run somatic variant calling on it.

   Annotations

   @ClpAnnotation()

5. class ExamplePipeline extends Pipeline

   

   Very simple example pipeline that is used in the README.md

   Very simple example pipeline that is used in the README.md

   Annotations

   @ClpAnnotation()

6. class GermlineVariantCallingPipeline extends Pipeline

   

   Pipeline to call germline variants in a set of regions

   Pipeline to call germline variants in a set of regions

   Annotations

   @ClpAnnotation()

7. class ParallelHaplotypeCaller extends Pipeline

   

   Annotations

   @ClpAnnotation()

8. class SomaticVariantCallingPipeline extends Pipeline

   

   Pipeline to call Somatic Variants using both Varscan2 and Mutect2

   Pipeline to call Somatic Variants using both Varscan2 and Mutect2

   Annotations

   @ClpAnnotation()