CFSAN SNP Pipeline¶
Contents:
- CFSAN SNP Pipeline
- SNP Pipeline Processes
- Installation
- Usage
- Correct and Reproducible Results
- FAQ / Troubleshooting Guide
- Configuration
- SnpPipeline_StopOnSampleError
- MaxConcurrentPrepSamples
- MaxConcurrentCallConsensus
- MaxConcurrentCollectSampleMetrics
- SnpPipeline_MaxSnps
- SnpPipeline_Aligner
- Bowtie2Build_ExtraParams
- SmaltIndex_ExtraParams
- SamtoolsFaidx_ExtraParams
- Bowtie2Align_ExtraParams
- SmaltAlign_ExtraParams
- SamtoolsSamFilter_ExtraParams
- SamtoolsSort_ExtraParams
- SnpPipeline_RemoveDuplicateReads
- PicardMarkDuplicates_ExtraParams
- PicardJvm_ExtraParams
- SamtoolsMpileup_ExtraParams
- VarscanMpileup2snp_ExtraParams
- VarscanJvm_ExtraParams
- RemoveAbnormalSnp_ExtraParams
- CreateSnpList_ExtraParams
- CallConsensus_ExtraParams
- CreateSnpMatrix_ExtraParams
- CreateSnpReferenceSeq_ExtraParams
- MergeVcf_ExtraParams
- BcftoolsMerge_ExtraParams
- CollectSampleMetrics_ExtraParams
- CombineSampleMetrics_ExtraParams
- Torque_StripJobArraySuffix
- GridEngine_StripJobArraySuffix
- GridEngine_PEname
- GridEngine_QsubExtraParams
- Torque_QsubExtraParams
- Command Reference
- Contributing
- Credits
- History
- 0.8.2 (2017-06-09) - docs
- 0.8.1 (2017-06-02) - docs
- 0.8.0 (2017-05-09) - docs
- 0.7.0 (2016-11-30) - docs
- 0.6.1 (2016-05-23)
- 0.6.0 (2016-04-11)
- 0.5.2 (2016-03-07)
- 0.5.1 (2016-02-19)
- 0.5.0 (2016-01-19)
- 0.4.1 (2015-10-30)
- 0.4.0 (2015-10-22)
- 0.3.4 (2015-06-25)
- 0.3.3 (2015-04-14)
- 0.3.2 (2015-01-14)
- 0.3.1 (2014-10-27)
- 0.3.0 (2014-10-22)
- 0.2.1 (2014-09-24)
- 0.2.0 (2014-09-17)
- 0.1.1 (2014-07-28)
- 0.1.0 (2014-07-03)