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| 1 | +# Basic PCGR configuration options (TOML). |
| 2 | + |
| 3 | +[tumor_only] |
| 4 | +## If input VCF contains mix of germline/somatic (variants called with no matching control, i.e. tumor-only) set vcf_tumor_only to true |
| 5 | +vcf_tumor_only = false |
| 6 | + |
| 7 | +## 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 |
| 8 | + |
| 9 | +## Exclude variants (SNVs/InDels) with minor allele frequency above the following population-specific thresholds |
| 10 | +## 1000 Genomes Project - WGS data |
| 11 | +maf_onekg_eur = 0.002 |
| 12 | +maf_onekg_amr = 0.002 |
| 13 | +maf_onekg_afr = 0.002 |
| 14 | +maf_onekg_sas = 0.002 |
| 15 | +maf_onekg_eas = 0.002 |
| 16 | +maf_onekg_global = 0.002 |
| 17 | + |
| 18 | +## exclude variants with minor allele frequency above the following population-specific thresholds |
| 19 | +## gnomAD - WES data |
| 20 | +maf_gnomad_nfe = 0.002 |
| 21 | +maf_gnomad_amr = 0.002 |
| 22 | +maf_gnomad_afr = 0.002 |
| 23 | +maf_gnomad_asj = 0.002 |
| 24 | +maf_gnomad_sas = 0.002 |
| 25 | +maf_gnomad_eas = 0.002 |
| 26 | +maf_gnomad_fin = 0.002 |
| 27 | +maf_gnomad_oth = 0.002 |
| 28 | +maf_gnomad_global = 0.002 |
| 29 | + |
| 30 | +## Exclude variants occurring in PoN (panel of normals, if provided as VCF) |
| 31 | +exclude_pon = true |
| 32 | + |
| 33 | +## Exclude likely homozygous germline variants (100% allelic fraction for alternate allele in tumor, very unlikely somatic event) |
| 34 | +exclude_likely_hom_germline = false |
| 35 | + |
| 36 | +## Exclude likely heterozygous germline variants |
| 37 | +## 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 |
| 38 | +## 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 |
| 39 | +## will be skewed (see e.g. discussion in PMID:29249243) |
| 40 | +exclude_likely_het_germline = false |
| 41 | + |
| 42 | +## Exclude variants found in dbSNP (only those that are NOT found in ClinVar(somatic origin)/DoCM/TCGA/COSMIC) |
| 43 | +exclude_dbsnp_nonsomatic = false |
| 44 | + |
| 45 | +## exclude all non-exonic variants |
| 46 | +exclude_nonexonic = true |
| 47 | + |
| 48 | +[allelic_support] |
| 49 | +## Specify INFO tags in input VCF that denotes depth/allelic fraction in tumor and normal sample |
| 50 | +## An additional tag that denotes call confidence (call_conf_tag) can also be specified, which will |
| 51 | +## be used for exploration in the global variant browser. Note that 'tumor_dp_tag' must be of |
| 52 | +## Type=Integer, and 'tumor_af_tag' must be of Type=Float (similarly for normal sample) |
| 53 | +tumor_dp_tag = "" |
| 54 | +tumor_af_tag = "" |
| 55 | +control_dp_tag = "" |
| 56 | +control_af_tag = "" |
| 57 | +call_conf_tag = "" |
| 58 | + |
| 59 | +## set thresholds for tumor depth/allelic fraction, will be applied before report generation |
| 60 | +## will only apply if 'tumor_dp_tag' and 'tumor_af_tag' are specified above (similarly |
| 61 | +## for 'control_dp_tag' and 'control_af_tag' |
| 62 | +tumor_dp_min = 0 |
| 63 | +tumor_af_min = 0.0 |
| 64 | +control_dp_min = 0 |
| 65 | +control_af_max = 1.0 |
| 66 | + |
| 67 | +[mutational_burden] |
| 68 | +## Calculate mutational burden (similar to Chalmers et al., Genome Med, 2017) |
| 69 | +mutational_burden = true |
| 70 | +## Size of coding target region in megabases (defaults to size of protein-coding regions of GENCODE ~ 34 Mb) |
| 71 | +## Note: this should ideally denote the callable target size (i.e. reflecting variable sequencing depth) |
| 72 | +target_size_mb = 34.0 |
| 73 | +## set upper limits to tumor mutational burden tertiles (mutations/Mb) |
| 74 | +tmb_low_limit = 5 |
| 75 | +tmb_intermediate_limit = 20 |
| 76 | +## tmb_high = tmb > tmb_intermediate_limit |
| 77 | + |
| 78 | +[cna] |
| 79 | +## log ratio thresholds for determination of copy number gains and homozygous deletions |
| 80 | +logR_gain = 0.8 |
| 81 | +logR_homdel = -0.8 |
| 82 | + |
| 83 | +## mean percent overlap between copy number segment and gene transcripts for reporting of gains/losses in tumor suppressor genes/oncogenes |
| 84 | +cna_overlap_pct = 50 |
| 85 | + |
| 86 | +[msi] |
| 87 | +## Predict microsatellite instability |
| 88 | +msi = true |
| 89 | + |
| 90 | +[mutational_signatures] |
| 91 | +## Identify relative contribution of 30 known mutational signatures (COSMIC) through the deconstructSigs framework |
| 92 | +mutsignatures = true |
| 93 | +## deconstructSigs option: number of mutational signatures to limit the search to ('signatures.limit' in whichSignatures) |
| 94 | +mutsignatures_signature_limit = 6 |
| 95 | +## deconstructSigs option: type of trimer count normalization for inference of known mutational signatures, see explanation at https://github.com/raerose01/deconstructSigs" |
| 96 | +## options = 'default', 'exome', 'genome', 'exome2genome' |
| 97 | +## NOTE: If your data (VCF) is from exome sequencing, 'default' or 'exome2genome' should be used. See https://github.com/raerose01/deconstructSigs/issues/2 |
| 98 | +mutsignatures_normalization = "exome2genome" |
| 99 | +## Require a minimum number of mutations for signature estimation |
| 100 | +mutsignatures_mutation_limit = 100 |
| 101 | +## deconstructSigs option: discard any signature contributions with a weight less than this amount |
| 102 | +mutsignatures_cutoff = 0.06 |
| 103 | + |
| 104 | +[visual] |
| 105 | +## Choose visual theme of report, any of: "default", "cerulean", "journal", "flatly", "readable", "spacelab", "united", "cosmo", "lumen", "paper", "sandstone", "simplex", or "yeti" (https://bootswatch.com/) |
| 106 | +report_theme = "default" |
| 107 | + |
| 108 | +[custom_tags] |
| 109 | +## list VCF info tags that should be present in JSON and TSV output |
| 110 | +## tags should be comma separated, i.e. custom_tags = "MUTECT2_FILTER,STRELKA_FILTER" |
| 111 | +custom_tags = "" |
| 112 | + |
| 113 | +[other] |
| 114 | +## list/do not list noncoding variants |
| 115 | +list_noncoding = true |
| 116 | +## VEP/vcfanno processing options |
| 117 | +n_vcfanno_proc = 4 |
| 118 | +n_vep_forks = 4 |
| 119 | +## 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) |
| 120 | +vep_pick_order = "canonical,appris,biotype,ccds,rank,tsl,length" |
| 121 | +## omit intergenic variants during VEP processing |
| 122 | +vep_skip_intergenic = false |
| 123 | +## generate a MAF for input VCF using https://github.com/mskcc/vcf2maf |
| 124 | +vcf2maf = true |
| 125 | + |
| 126 | +## Not for edit |
| 127 | +[tumor_type] |
| 128 | +type = "" |
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