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ACCESS_variant_calling_parameters.yaml
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| # Params | |
| mutect_params: | |
| dcov: 5000 | |
| read_filter: ['BadCigar'] | |
| fraction_contamination: 0.0005 | |
| minimum_mutation_cell_fraction: 0.0005 | |
| vardict_params: | |
| allele_freq_thres: 0.0005 | |
| min_num_variant_reads: 1 | |
| column_for_region_end: 3 | |
| column_for_chromosome: 1 | |
| column_for_gene_name: 4 | |
| column_for_region_start: 2 | |
| basicfiltering_mutect_params: | |
| total_depth: 20 | |
| allele_depth: 1 | |
| variant_fraction: 0.00005 | |
| tumor_normal_ratio: 1 | |
| outdir: . | |
| basicfiltering_vardict_params: | |
| min_qual: 0 | |
| total_depth: 20 | |
| allele_depth: 1 | |
| tumor_normal_ratio: 1 | |
| filter_germline: false | |
| variant_fraction: 0.00005 | |
| outdir: . | |
| bcftools_params: | |
| allow_overlaps: true | |
| rm_dups: all | |
| vcf2maf_params: | |
| vep_forks: 4 | |
| buffer_size: 5000 | |
| max_filter_ac: 10 | |
| min_hom_vaf: 0.7 | |
| ncbi_build: GRCh37 | |
| retain_info: 'set,TYPE,FAILURE_REASON,MUTECT,VCF_POS,VCF_REF,VCF_ALT' | |
| maf_center: mskcc.org | |
| species: homo_sapiens_merged | |
| gbcms_params: | |
| maq: 20 | |
| thread: 10 | |
| omaf: true | |
| fragment_count: 1 | |
| filter_duplicate: 0 | |
| access_filters_params: | |
| tumor_TD_min: 20 # Tumor Min Depth | |
| normal_TD_min: 20 # Normal Min Depth | |
| tn_ratio_thres: 2 # Tumor Normal Ratio threshold | |
| tier_one_alt_min: 3 | |
| tier_two_alt_min: 5 | |
| tumor_detect_alt_thres: 2 | |
| curated_detect_alt_thres: 2 | |
| DS_tumor_detect_alt_thres: 2 # Duplex Simplex alt allele threshold | |
| DS_curated_detect_alt_thres: 2 # Duplex Simplex Curated alt allele threshold | |
| tumor_vaf_germline_thres: 0 | |
| normal_vaf_germline_thres: 0.3 | |
| min_n_curated_samples_alt_detected: 2 |
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