args

Type Members

1. trait Arguments extends Base

   Common command-line arguments for loading in one or more sets of reads, and associating a sample-name with each.

2. trait Base extends ReadFilterArgs with NoSequenceDictionaryArgs

3. trait GermlineCallerArgs extends Args4jBase with Args with GenotypeOutputArgs with SingleSampleArgs with ConcordanceArgs

4. trait HasReference extends AnyRef

5. trait NoSequenceDictionaryArgs extends AnyRef

   Argument for using / not using sequence dictionaries to get contigs and lengths.

6. trait ReferenceArgs extends HasReference

7. trait SingleSampleArgs extends Base with ReadFilterArgs

   Argument for accepting a single set of reads (for non-somatic variant calling).

8. trait TumorNormalReadsArgs extends Base with ReadFilterArgs

   Arguments for accepting two sets of reads (tumor + normal).