bwa

Type Members

1. class BwaAln extends ProcessTask with VariableResources

   

   Class for running "bwa aln"

2. class BwaBacktrack extends Pipeline

   

   Pipeline that starts with an unmapped BAM and runs through conversion to fastq, running bwa aln, bwa sampe and then MergeBamAlignment to generate a tidy mapped BAM file via bwa backtrack/bwa short alignment.

3. class BwaIndex extends ProcessTask with FixedResources

   

   Indexes a genome for use with BWA.

4. class BwaK8AltProcessor extends ProcessTask with FixedResources with Configuration with Pipe[Sam, Sam]

   

   Task for running the alt-mapping post-processing setup from bwa.kit.

   Task for running the alt-mapping post-processing setup from bwa.kit. By default reads from stdin, but an input file can be supplied. Writes to stdout.

5. class BwaMem extends ProcessTask with VariableResources with Pipe[Fastq, Sam]

   

6. class BwaSampe extends ProcessTask with FixedResources

   

   Class for running "bwa sampe"

7. class BwaSamse extends ProcessTask with FixedResources

   

   Class for running "bwa samse"