pipeline5
Created: 2015-01-09 06:42:11
Last updated: 2015-01-09 06:43:09
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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
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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)
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