MutSigWithNozzleReport

MutSigPreprocess1 individual_set_id	OV
MutSigPreprocess1 maf1	MutSigPreprocess1.maf1.input.tsv
MutSigPreprocess1 maf2	MutSigPreprocess1.maf2.input.tsv
MutSigPreprocess1 maf3	MutSigPreprocess1.maf3.input.tsv
MutSigPreprocess1 maflabel1	Broad
MutSigPreprocess1 maflabel2	WashU
MutSigPreprocess1 maflabel3	Baylor
MutSigPreprocess1 wig1	MutSigPreprocess1.wig1.input.tsv
MutSigPreprocess1 wig2	MutSigPreprocess1.wig2.input.tsv
MutSigPreprocess1 wig3	MutSigPreprocess1.wig3.input.tsv
MutSigPreprocess1 build	hg18
MutSigPreprocess1 context65_dir	/xchip/cga1/lawrence/db/context65
MutSigPreprocess1 build_dir	/xchip/cga1/annotation/db/ucsc/hg18
MutSigPreprocess1 num_categories	4
MutSigPreprocess1 target_list	/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
MutSigPreprocess1 paramfile	/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
MutSigRun3 individual_set_id	OV
MutSigRun3 gene_list	/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt
MutSigRun3 build	hg18
MutSigRun3 geneset_file	/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
MutSigRun3 cosmic_file	/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
MutSigRun3 refseq_file	/xchip/cga1/annotation/db/ucsc/hg18/R.mat
MutSigRun3 build_dir	/xchip/cga1/annotation/db/ucsc/hg18
MutSigRun3 param_file	/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
MutSigRun3 jobcount	200
CoMut4 individualSetId	OV
GDAC_MutSig_Report6 ind_set	OV

individual_set_id	OV
maf1	MutSigPreprocess1.maf1.input.tsv
maf2	MutSigPreprocess1.maf2.input.tsv
maf3	MutSigPreprocess1.maf3.input.tsv
maf4
maflabel1	Broad
maflabel2	WashU
maflabel3	Baylor
maflabel4
wig1	MutSigPreprocess1.wig1.input.tsv
wig2	MutSigPreprocess1.wig2.input.tsv
wig3	MutSigPreprocess1.wig3.input.tsv
wig4
build	hg18
context65_dir	/xchip/cga1/lawrence/db/context65
build_dir	/xchip/cga1/annotation/db/ucsc/hg18
num_categories	4
target_list	/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
paramfile	/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt

Output Files:
	OV.mutation_preprocessing_report.txt
	OV.patients.txt
	OV.maf
	OV.coverage.prepare.txt
	.lsf.out
	stdout.txt

step 2. ProcessCoverageForMutSig [id: 144828] processes coverage from wiggle files and does automatic category discovery

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00188:77

step 3. MutSigRun [id: 144829] perform MutSig calculations, generates output tables and report

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00286:160

individual_set_id	OV
mutation_file	OV.maf
coverage_file	OV.coverage.mat
patient_file	OV.patients.txt
category_file	OV.mutcategs.txt
gene_list	/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt
build	hg18
geneset_file	/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
cosmic_file	/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
refseq_file	/xchip/cga1/annotation/db/ucsc/hg18/R.mat
build_dir	/xchip/cga1/annotation/db/ucsc/hg18
param_file	/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
mutation_preprocessing_report_file	OV.mutation_preprocessing_report.txt
jobcount	200

Output Files:
	jobName.txt
	.lsf.out
	stderr.txt
	java.opts
	OV.mutation_filtering_report.txt
	OV.MutSig_version.txt
	OV.per_exon.coverage.txt
	OV.covplot.png
	OV.patients.counts_and_rates.txt
	OV.covplot_hires.png
	OV.bargraphs.png
	OV.num_patients.txt
	OV.bargraphs_hires.png
	OV.final_analysis_set.maf
	OV.mutcategs.txt
	OV.per_gene.coverage.txt
	OV.per_gene.mutation_counts.txt
	OV.mutation_breakdown.txt
	OV.mutsig2.images
	OV.sample_sig_gene_table.txt
	OV.mutation_rates.txt
	OV.sig_genes.txt
	OV.sig_genesets.txt
	OV.sig_genesets_2.txt
	OV.cosmic_sig_genes.txt
	OV.cosmic_mutations.txt_verbose.txt
	OV.cosmic_sig_genes2.txt
	OV.cosmic_mutations.txt
	OV.clustered_muts.txt
	OV.gene_gene_correlations.txt
	OV.power_per_gene.total_coverage.txt
	OV.power_per_gene.total_coverage_histogram
	OV.power_per_gene.power_stats.txt
	OV.power_per_gene.power_stats_full.txt
	OV.power_per_gene.power_summary.txt
	OV.gene_coverage_plots
	finished
	jobSubmissions.txt
	iterator.out.txt
	stdout.txt

step 4. CoMut [id: 144830]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00488:7

individualSetId	OV
patientCRFile	OV.patients.counts_and_rates.txt
mafFile	OV.final_analysis_set.maf
mutcategsFile	OV.mutcategs.txt
sigGenesFile	OV.sig_genes.txt

step 5. GenerateStickFigures [id: 144831]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00497:4

maf	OV.final_analysis_set.maf
sig_genes	OV.sig_genes.txt

Output Files:
	generatedStickFigurePaths.txt
	.lsf.out
	stdout.txt

step 6. GDAC_MutSig_Report [id: 144832] Somatic Mutation Report

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00413:16

bar_plot	OV.bargraphs.png
breakdown_table	OV.mutation_breakdown.txt
categories_table	OV.mutation_rates.txt
coverage png	OV.covplot.png
sig_table	OV.sig_genes.txt
cosmic_table	OV.cosmic_sig_genes.txt
cosmic_table2	OV.cosmic_sig_genes2.txt
cosmic_muts_table	OV.cosmic_mutations.txt
cluster_table	OV.clustered_muts.txt
geneset_table	OV.sig_genesets.txt
genset_table2	OV.sig_genesets_2.txt
patients_c_and_r	OV.patients.counts_and_rates.txt
ind_set	OV
mutsig_version	OV.MutSig_version.txt
coMut_plot_png	OV_coMut.png
coMut_plot_pdf	OV_coMut.pdf
stick_figures_path	generatedStickFigurePaths.txt
maf_path	OV.final_analysis_set.maf
mut_pre_rep_path	OV.mutation_preprocessing_report.txt
mut_filt_rep_path	OV.mutation_filtering_report.txt

MutSigWithNozzleReport Execution Log 8:31 AM Fri Aug 10, '12