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| # Basic PCGR configuration options (TOML). | ||
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| [tumor_only] | ||
| ## If input VCF contains mix of germline/somatic (variants called with no matching control, i.e. tumor-only) set vcf_tumor_only to true | ||
| vcf_tumor_only = false | ||
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| ## If vcf_tumor_only = true, several filters can be configured, all as a means to minimize the proportion of germline calls in the raw set derived from tumor-only calling | ||
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| ## Exclude variants (SNVs/InDels) with minor allele frequency above the following population-specific thresholds | ||
| ## 1000 Genomes Project - WGS data | ||
| maf_onekg_eur = 0.002 | ||
| maf_onekg_amr = 0.002 | ||
| maf_onekg_afr = 0.002 | ||
| maf_onekg_sas = 0.002 | ||
| maf_onekg_eas = 0.002 | ||
| maf_onekg_global = 0.002 | ||
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| ## exclude variants with minor allele frequency above the following population-specific thresholds | ||
| ## gnomAD - WES data | ||
| maf_gnomad_nfe = 0.002 | ||
| maf_gnomad_amr = 0.002 | ||
| maf_gnomad_afr = 0.002 | ||
| maf_gnomad_asj = 0.002 | ||
| maf_gnomad_sas = 0.002 | ||
| maf_gnomad_eas = 0.002 | ||
| maf_gnomad_fin = 0.002 | ||
| maf_gnomad_oth = 0.002 | ||
| maf_gnomad_global = 0.002 | ||
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| ## Exclude variants occurring in PoN (panel of normals, if provided as VCF) | ||
| exclude_pon = true | ||
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| ## Exclude likely homozygous germline variants (100% allelic fraction for alternate allele in tumor, very unlikely somatic event) | ||
| exclude_likely_hom_germline = false | ||
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| ## Exclude likely heterozygous germline variants | ||
| ## Must satisfy i) 40-60 % allelic fraction for alternate allele in tumor sample, ii) present in dbSNP + gnomAD, ii) not existing as somatic event in COSMIC/TCGA | ||
| ## Note that the application of this filter may be suboptimal for very impure tumors or variants affected by CNAs etc (under these circumstances, the allelic fraction | ||
| ## will be skewed (see e.g. discussion in PMID:29249243) | ||
| exclude_likely_het_germline = false | ||
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| ## Exclude variants found in dbSNP (only those that are NOT found in ClinVar(somatic origin)/DoCM/TCGA/COSMIC) | ||
| exclude_dbsnp_nonsomatic = false | ||
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| ## exclude all non-exonic variants | ||
| exclude_nonexonic = true | ||
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| [allelic_support] | ||
| ## Specify INFO tags in input VCF that denotes depth/allelic fraction in tumor and normal sample | ||
| ## An additional tag that denotes call confidence (call_conf_tag) can also be specified, which will | ||
| ## be used for exploration in the global variant browser. Note that 'tumor_dp_tag' must be of | ||
| ## Type=Integer, and 'tumor_af_tag' must be of Type=Float (similarly for normal sample) | ||
| tumor_dp_tag = "" | ||
| tumor_af_tag = "" | ||
| control_dp_tag = "" | ||
| control_af_tag = "" | ||
| call_conf_tag = "" | ||
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| ## set thresholds for tumor depth/allelic fraction, will be applied before report generation | ||
| ## will only apply if 'tumor_dp_tag' and 'tumor_af_tag' are specified above (similarly | ||
| ## for 'control_dp_tag' and 'control_af_tag' | ||
| tumor_dp_min = 0 | ||
| tumor_af_min = 0.0 | ||
| control_dp_min = 0 | ||
| control_af_max = 1.0 | ||
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| [mutational_burden] | ||
| ## Calculate mutational burden (similar to Chalmers et al., Genome Med, 2017) | ||
| mutational_burden = true | ||
| ## Size of coding target region in megabases (defaults to size of protein-coding regions of GENCODE ~ 34 Mb) | ||
| ## Note: this should ideally denote the callable target size (i.e. reflecting variable sequencing depth) | ||
| target_size_mb = 34.0 | ||
| ## set upper limits to tumor mutational burden tertiles (mutations/Mb) | ||
| tmb_low_limit = 5 | ||
| tmb_intermediate_limit = 20 | ||
| ## tmb_high = tmb > tmb_intermediate_limit | ||
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| [cna] | ||
| ## log ratio thresholds for determination of copy number gains and homozygous deletions | ||
| logR_gain = 0.8 | ||
| logR_homdel = -0.8 | ||
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| ## mean percent overlap between copy number segment and gene transcripts for reporting of gains/losses in tumor suppressor genes/oncogenes | ||
| cna_overlap_pct = 50 | ||
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| [msi] | ||
| ## Predict microsatellite instability | ||
| msi = true | ||
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| [mutational_signatures] | ||
| ## Identify relative contribution of 30 known mutational signatures (COSMIC) through the deconstructSigs framework | ||
| mutsignatures = true | ||
| ## deconstructSigs option: number of mutational signatures to limit the search to ('signatures.limit' in whichSignatures) | ||
| mutsignatures_signature_limit = 6 | ||
| ## deconstructSigs option: type of trimer count normalization for inference of known mutational signatures, see explanation at https://github.com/raerose01/deconstructSigs" | ||
| ## options = 'default', 'exome', 'genome', 'exome2genome' | ||
| ## NOTE: If your data (VCF) is from exome sequencing, 'default' or 'exome2genome' should be used. See https://github.com/raerose01/deconstructSigs/issues/2 | ||
| mutsignatures_normalization = "exome2genome" | ||
| ## Require a minimum number of mutations for signature estimation | ||
| mutsignatures_mutation_limit = 100 | ||
| ## deconstructSigs option: discard any signature contributions with a weight less than this amount | ||
| mutsignatures_cutoff = 0.06 | ||
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| [visual] | ||
| ## Choose visual theme of report, any of: "default", "cerulean", "journal", "flatly", "readable", "spacelab", "united", "cosmo", "lumen", "paper", "sandstone", "simplex", or "yeti" (https://bootswatch.com/) | ||
| report_theme = "default" | ||
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| [custom_tags] | ||
| ## list VCF info tags that should be present in JSON and TSV output | ||
| ## tags should be comma separated, i.e. custom_tags = "MUTECT2_FILTER,STRELKA_FILTER" | ||
| custom_tags = "" | ||
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| [other] | ||
| ## list/do not list noncoding variants | ||
| list_noncoding = true | ||
| ## VEP/vcfanno processing options | ||
| n_vcfanno_proc = 4 | ||
| n_vep_forks = 4 | ||
| ## Customise the order of criteria used to pick the primary transcript in VEP (see https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_pick_order) | ||
| vep_pick_order = "canonical,appris,biotype,ccds,rank,tsl,length" | ||
| ## omit intergenic variants during VEP processing | ||
| vep_skip_intergenic = false | ||
| ## generate a MAF for input VCF using https://github.com/mskcc/vcf2maf | ||
| vcf2maf = true | ||
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| ## Not for edit | ||
| [tumor_type] | ||
| type = "" |
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| # Sphinx build info version 1 | ||
| # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. | ||
| config: 1b5753ec6635113bf8ca74c36d47b914 | ||
| config: 21394eecc26621110784fc2eac7a29dc | ||
| tags: 645f666f9bcd5a90fca523b33c5a78b7 |
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