pipeline5
Created: 2015-01-09 06:42:11
Last updated: 2015-01-09 06:43:09
Download Workflow
Preview
Not available
Import
Not currently available.
Workflow Components
Inputs (70)
| Name | Description |
|---|---|
| Population VCF | Population VCF |
| Genotype VCF hg 14002 | Genotype VCF hg 14002 |
| dindel_path | runtime parameter for tool Dindel |
| pythonFilePath | runtime parameter for tool Dindel |
| outptDir | runtime parameter for tool Dindel |
| contEst_path | runtime parameter for tool contEst |
| OutputDir | runtime parameter for tool contEst |
| COPS_Script_Location | runtime parameter for tool COPS |
| chr | runtime parameter for tool COPS |
| Output_Dir | runtime parameter for tool COPS |
| Output_Dir | runtime parameter for tool indelocator |
| indelocator_script_location | runtime parameter for tool indelocator |
| maxThreads | runtime parameter for tool Control FREEC |
| ploidy | runtime parameter for tool Control FREEC |
| toolPath | runtime parameter for tool Control FREEC |
| printNA | runtime parameter for tool Control FREEC |
| window | runtime parameter for tool Control FREEC |
| noisyData | runtime parameter for tool Control FREEC |
| Output_Dir | runtime parameter for tool Control FREEC |
| sample_mateOrientation | runtime parameter for tool Control FREEC |
| control_inputFormat | runtime parameter for tool Control FREEC |
| step | runtime parameter for tool Control FREEC |
| sample_inputFormat | runtime parameter for tool Control FREEC |
| contaminationAdjustment | runtime parameter for tool Control FREEC |
| control_mateOrientation | runtime parameter for tool Control FREEC |
| readCountThreshold | runtime parameter for tool Control FREEC |
| breakPointThreshold | runtime parameter for tool Control FREEC |
| chrFiles | runtime parameter for tool Control FREEC |
| samtoolsPath | runtime parameter for tool Control FREEC |
| SampleName | runtime parameter for tool music2_all |
| Output_Dir | runtime parameter for tool music2_all |
| path_for_all_Input_files | runtime parameter for tool Indel_OSCC |
| GATK_Path | runtime parameter for tool Indel_OSCC |
| VEP_Path | runtime parameter for tool Indel_OSCC |
| VCF_Tools_path | runtime parameter for tool Indel_OSCC |
| SampleName | runtime parameter for tool Indel_OSCC |
| Output_Dir | runtime parameter for tool Indel_OSCC |
| 1000G | 1000G |
| reference_build | runtime parameter for tool Annovar |
| file_format | runtime parameter for tool Annovar |
| dbtype | runtime parameter for tool Annovar |
| humandb_path | runtime parameter for tool Annovar |
| Output_Dir | runtime parameter for tool Annovar |
| Annovar_tool_path | runtime parameter for tool Annovar |
| Intogen_path | runtime parameter for tool Intogen |
| analysis | runtime parameter for tool Intogen |
| workspace | runtime parameter for tool Intogen |
| species | runtime parameter for tool ENSEMBL variant effect predictor |
| Output_Dir | runtime parameter for tool Cravat |
| chasmClassifier | runtime parameter for tool Cravat |
| runtime parameter for tool Cravat | |
| Hg19 | |
| dbsnp | |
| gatk_location | runtime parameter for tool GATK2_CJ |
| prefix | runtime parameter for tool GATK2_CJ |
| outputFolder | runtime parameter for tool GATK2_CJ |
| rgTag | runtime parameter for tool GATK2_CJ |
| gatk_location | runtime parameter for tool GATK2_CJ |
| prefix | runtime parameter for tool GATK2_CJ |
| outputFolder | runtime parameter for tool GATK2_CJ |
| rgTag | runtime parameter for tool GATK2_CJ |
| gatk_path | runtime parameter for tool Filter post VCF |
| Sample_Name | runtime parameter for tool Filter post VCF |
| IntersectBed_Path | runtime parameter for tool Filter post VCF |
| output_Dir | runtime parameter for tool Filter post VCF |
| dindel_path | runtime parameter for tool Dindel |
| pythonFilePath | runtime parameter for tool Dindel |
| outptDir | runtime parameter for tool Dindel |
| contEst_path | runtime parameter for tool contEst |
| OutputDir | runtime parameter for tool contEst |
Steps (25)
| Name | Tool | Description |
|---|---|---|
| Input dataset | None | |
| Input dataset | None | |
| merge Location File post GATK | merge Location File post GATK | |
| Dindel | Dindel | |
| contEst | contEst | |
| COPS | COPS | |
| indelocator | indelocator | |
| Control FREEC | Control FREEC | |
| music2_all | music2_all | |
| Indel_OSCC | Indel_OSCC | |
| Merge VCF | Merge VCF | |
| vcf_to_cravat | vcf_to_cravat | |
| Input dataset | None | |
| Annovar | Annovar | |
| Intogen | Intogen | |
| ENSEMBL variant effect predictor | toolshed.g2.bx.psu.edu/repos/alonie/ensembl_vep/ensembl/1.0.0 | |
| Cravat | Cravat | |
| Visualization of post Intogen | Visualization of post Intogen | |
| Input dataset | None | |
| Input dataset | None | |
| GATK2_CJ | GATK2_CJ | |
| GATK2_CJ | GATK2_CJ | |
| Filter post VCF | Filter post VCF | |
| Dindel | Dindel | |
| contEst | contEst |
Outputs (70)
| Name | Type |
|---|---|
| o_merged_locationFile_post_GATK | tabular |
| o_variantCalls | vcf |
| o_outputFL | tabular |
| stdErr_stdOut | txt |
| o_ouput | tabular |
| o_outputFL | tabular |
| o_output | txt |
| o_logFile | txt |
| o_outputFL | tabular |
| o_indelocator_vcf | vcf |
| o_outputFL | tabular |
| o_stderr_stdout | txt |
| o_CNVs | txt |
| o_ratio | txt |
| o_sample | txt |
| o_control | txt |
| o_outputFL | tabular |
| o_roi_covg | txt |
| o_gene_covg | txt |
| o_total_covgs | txt |
| o_overall_bmrs | txt |
| o_gene_mrs | txt |
| o_gene_mrs_for_R | txt |
| o_outputFL | tabular |
| o_Indel_OSCC_output_File_VCF | vcf |
| o_outputFL | txt |
| stdout | txt |
| mergedVCF | vcf |
| o_input_ready_for_cravat | vcf |
| o_log_file | txt |
| o_invalid_input | txt |
| o_filtered | tabular |
| o_dropped | tabular |
| o_locationFile | tabular |
| o_consequences | txt |
| o_fimpactGitools | txt |
| o_genes | txt |
| o_pathways | txt |
| o_project | txt |
| o_variantGenes | txt |
| o_variantSamples | txt |
| stdErr_stdOut | txt |
| o_outputFL | tabular |
| output | tabular |
| o_errorFile | txt |
| o_driverAnalysis | xls |
| o_Codon_Level_Analysis | tabular |
| o_Gene_Level_Analysis | tabular |
| o_Variant_Analysis | tabular |
| o_MuPIT_Interactive_input | tabular |
| o_outputFL | tabular |
| STDERR | txt |
| visualize_post_Intogen | csv |
| o_log_file | txt |
| o_raw_vcf | vcf |
| o_BAM | bam |
| o_Bam_bai | txt |
| gatk_output_location_file | tabular |
| o_log_file | txt |
| o_raw_vcf | vcf |
| o_BAM | bam |
| o_Bam_bai | txt |
| gatk_output_location_file | tabular |
| o_outputCallableAlt | vcf |
| o_outputFL | tabular |
| o_variantCalls | vcf |
| o_outputFL | tabular |
| stdErr_stdOut | txt |
| o_ouput | tabular |
| o_outputFL | tabular |
Workflow Type
Version 1
(of 1)
Shared with Groups (0)
None
Statistics
Version History
In chronological order:
-
Created by Chetan Joshi on Friday 09 January 2015 06:42:10 (UTC)
Last edited by Chetan Joshi on Friday 09 January 2015 06:43:09 (UTC)
Reviews
(0)
Other workflows that use similar services
(0)
There are no workflows in myExperiment that use similar services to this Workflow.
No comments yet
Log in to make a comment