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fileDirectory.txt
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fileDirectory.txt
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fileDescriptor path verboseDescription generatingScript
#Directory of files in hypermutation project. This file is parsed by a utility script. Note all lines that start with # are ignored. The first line needs to be a header
####FILES
#-------------INFO FILES
HYPERMUTATION_STATUS_IDS files/hypermutationStatusIds all cases by cancer type and with their hypermutation status scriptToDoIds
CANCER_TYPE_INFO files/infoFiles/cancerTypeInfo.txt information about cancer-type and tmb generated by chai
TCGA_CANCER_TYPE_INFO files/infoFiles/tcgaCancerTypeInfo.txt
GENE_LENGTH_INFO files/infoFiles/all_gene_coding_sequences.tsv
CASE_TMB_AND_MSI_STATS files/infoFiles/mutations_TMB_and_MSI_stats.txt
DEP_MAP_DATA files/infoFiles/projectAchillesDepMapData.csv
PHASING_DATA files/infoFiles/mutation_phasing_data.txt
HOTSPOT_DATA files/infoFiles/hotspots_data.txt
MICROSATELLITE_INFORMATION files/infoFiles/impact_microsatellites.txt
DNDS_RESULTS files/infoFiles/dndsHypermutants.tsv
PHASING_SUMMARY files/infoFiles/phasingSummary.tsv
TCGA_MSI_SCORES files/infoFiles/tcgaMsiScores.txt
NUCLEOSOME_DYAD_POSITIONS files/infoFiles/dyads_genic.bed.txt
GTEX_DATA files/infoFiles/GTEX_TPM_DATA.gct
REPLICATION_TIMING_DATA files/infoFiles/replication_timing.csv
TABLE_5 files/infoFiles/dndsData.tsv
CANCER_PATHWAY_DATA files/infoFiles/cancerPathways.csv
#-------------EXPECTATION
ALL_POSSIBLE_MUTATION_SUMMARY files/expectedMutationInfo/allPossibleIMPACTMutationsSummary.tsv
EXPECTED_MUTATION_INFO_BY_GENE files/expectedMutationInfo/allHypermutatorsExpectedGeneMutInfo.tsv
TCGA_EXPECTED_MUTATION_INFO files/expectedMutationInfo/tcgaExpectedMutationInfo.tsv
###########--------------SIGNATURES
SIGNATURE_SPECTRUM files/infoFiles/Stratton_signatures30.txt
IMPACT_SIGNATURE_DECOMPOSITIONS files/infoFiles/impactSignatureCalls_Nov20_2019.tsv
TCGA_SIGNATURE_DECOMPOSITIONS files/infoFiles/tcgaSigDecomposition.txt
EXOME_RECAPTURE_SIGNATURE_DECOMPOSITIONS files/infoFiles/exomeRecaptureSigDecomposition.tsv
BRANCH_MUTATIONAL_SIGNATURES /files/infoFiles/branchMutationalSignatures.tsv
CLONAL_VS_SUBCLONAL_MUTATIONAL_SIGNATURES /files/infoFiles/clonalVsSubclonalMutationalSignatures.txt
SIGNATURE_ATTRIBUTION files/mafs/sigAttribution_hypermutators.tsv
#-------------MAFS
IMPACT_BASE_MAF files/mafs/impact_mutations_maf_filtered
IMPACT_BASE_MAF_WITH_SYNONYMOUS files/mafs/impact_mutations_maf_synonymous_included.maf NOTE_THIS_IS_A_CSV
ALL_EXOME_MAF files/mafs/allExomeMaf.maf
ALL_EXOME_HYPERMUTATOR_MAF files/mafs/allHypermutatorsExome.maf
ALL_EXOME_HYPERMUTATOR_MAF_WITH_TRINUC files/mafs/allHypermutatorExomeWithTrinuc.maf
IMPACT_MAF_WITH_CNCF_ANNOTATION files/mafs/combined_cncf_annotated.maf
IMPACT_MAF_WITH_ADJUSTED_CLONALITY_ANNOTATION files/mafs/combined_cncf_hypermutants_adjusted_annotated.maf
MAF_WITH_MUTATION_ATTRIBUTION files/mafs/mafWithMutationAttribution.tsv
HYPERMUTANT_MAF_WITH_TIMING_INFORMATION files/mafs/hypermutantTimingMaf.maf
PENTANUCLEOTIDE_CONTEXT_ANNOTATED_MAF files/mafs/poleCaseMafWithPentanucleotideContext.maf
BRANCH_ANNOTATED_MAF files/mafs/hypermutantMultipleSamplesLabeledByBranch.tsv
####UTILITY SCRIPTS
SCRIPT_DEFINE_HYPERMUTATION_THRESHOLDS scripts/utilityScripts/plotAndDefineHypermutationThresholds.R
SCRIPT_RUN_MUTATIONAL_SIGNATURES
SCRIPT_ATTRIBUTE_MUTATIONS_TO_SIGNATURES scripts/utilityScripts/attribute_mutations_to_signatures.py
SCRIPT_RUN_DNDS_CV scripts/utilityScripts/runDnDsCv.R
SCRIPT_ADJUST_CLONALITY_CALLS scripts/utilityScripts/adjust_clonality_calls_for_hypermutators.py
SCRIPT_SUMMARIZE_ALL_POSSIBLE_MUTATION_MAFS scripts/utilityScripts/summarize_possible_mutations.py
SCRIPT_COUNT_MUTATION_TYPE scripts/utilityScripts/count_mutation_type_from_sim_mafs.py
##FIGURE TABLES
TABLE_1_IMPACT_DATA_SUMMARY
##FIGURE 1
##FIGURE 2
##FIGURE 3