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Merge pull request #1504 from mskcc/master
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2 parents 980e503 + 6e491e3 commit c059d18

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‎beagle/__init__.py‎

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__version__ = "2.1.1"
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__version__ = "2.1.2"

‎runner/operator/access/heme/snps_and_indels/input_template.json.jinja2‎

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{
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"version": "1.3.40",
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"project_name": "access_legacy_snv_pipeline",
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"tumor_bams": {{ tumor_bams }},
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"normal_bams": {{ normal_bams }},
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"tumor_sample_names": {{ tumor_sample_names }},
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"normal_sample_names": {{ normal_sample_names }},
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"matched_normal_ids": {{ matched_normal_ids }},
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"genotyping_bams": {{ genotyping_bams }},
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"genotyping_bams_ids": {{ genotyping_bams_ids }},
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"tumor_bams": {{tumor_bams}},
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"normal_bams": {{normal_bams}},
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"tumor_sample_names": {{tumor_sample_names}},
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"normal_sample_names": {{normal_sample_names}},
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"matched_normal_ids": {{matched_normal_ids}},
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"genotyping_bams": {{genotyping_bams}},
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"genotyping_bams_ids": {{genotyping_bams_ids}},
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"mutect_params": {
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"dcov": 5000,
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"read_filter": ["BadCigar"],
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"fraction_contamination": 0.0005,
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"minimum_mutation_cell_fraction": 0.0005
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"dcov": 5000,
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"read_filter": ["BadCigar"],
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"fraction_contamination": 0.0005,
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"minimum_mutation_cell_fraction": 0.0005,
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},
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"vardict_params": {
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"allele_freq_thres": 0.0002,
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"min_num_variant_reads": 1,
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"column_for_region_end": 3,
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"column_for_chromosome": 1,
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"column_for_gene_name": 4,
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"column_for_region_start": 2
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"allele_freq_thres": 0.0002,
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"min_num_variant_reads": 1,
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"column_for_region_end": 3,
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"column_for_chromosome": 1,
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"column_for_gene_name": 4,
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"column_for_region_start": 2,
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},
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"basicfiltering_mutect_params": {
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"total_depth": 20,
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"allele_depth": 1,
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"variant_fraction": 0.00005,
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"tumor_normal_ratio": 1,
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"outdir": "."
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"total_depth": 20,
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"allele_depth": 1,
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"variant_fraction": 0.00005,
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"tumor_normal_ratio": 1,
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"outdir": ".",
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},
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"basicfiltering_vardict_params": {
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"min_qual": 0,
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"total_depth": 20,
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"allele_depth": 1,
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"tumor_normal_ratio": 1,
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"filter_germline": false,
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"variant_fraction": 0.00005,
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"outdir": "."
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},
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"bcftools_params": {
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"allow_overlaps": true,
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"rm_dups": "none"
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},
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"min_qual": 0,
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"total_depth": 20,
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"allele_depth": 1,
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"tumor_normal_ratio": 1,
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"filter_germline": false,
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"variant_fraction": 0.00005,
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"outdir": ".",
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},
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"bcftools_params": {"allow_overlaps": true, "rm_dups": "none"},
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"vcf2maf_params": {
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"vep_forks": 4,
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"buffer_size": 5000,
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"max_filter_ac": 10,
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"min_hom_vaf": 0.7,
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"ncbi_build": "GRCh37",
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"retain_info": "set,TYPE,FAILURE_REASON,MUTECT,VCF_POS,VCF_REF,VCF_ALT",
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"maf_center": "mskcc.org",
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"species": "homo_sapiens_merged"
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},
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"gbcms_params": {
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"maq": 20,
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"thread": 10,
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"omaf": true,
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"fragment_count": 1,
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"filter_duplicate": 0
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},
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"vep_forks": 4,
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"buffer_size": 5000,
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"max_filter_ac": 10,
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"min_hom_vaf": 0.7,
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"ncbi_build": "GRCh37",
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"retain_info": "set,TYPE,FAILURE_REASON,MUTECT,VCF_POS,VCF_REF,VCF_ALT",
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"maf_center": "mskcc.org",
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"species": "homo_sapiens_merged",
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},
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"gbcms_params": {"maq": 20, "thread": 10, "omaf": true, "fragment_count": 1, "filter_duplicate": 0},
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"access_filters_params": {
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"tumor_TD_min": 20,
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"normal_TD_min": 20,
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"tn_ratio_thres": 2,
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"tier_one_alt_min": 3,
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"tier_two_alt_min": 5,
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"tumor_detect_alt_thres": 2,
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"curated_detect_alt_thres": 2,
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"DS_tumor_detect_alt_thres": 2,
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"DS_curated_detect_alt_thres": 2,
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"tumor_vaf_germline_thres": 0,
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"normal_vaf_germline_thres": 0.3,
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"min_n_curated_samples_alt_detected": 2
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"tumor_TD_min": 20,
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"normal_TD_min": 20,
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"tn_ratio_thres": 2,
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"tier_one_alt_min": 3,
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"tier_two_alt_min": 5,
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"tumor_detect_alt_thres": 2,
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"curated_detect_alt_thres": 2,
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"DS_tumor_detect_alt_thres": 2,
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"DS_curated_detect_alt_thres": 2,
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"tumor_vaf_germline_thres": 0,
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"normal_vaf_germline_thres": 0.3,
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"min_n_curated_samples_alt_detected": 2,
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},
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"dbsnp": {
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"class": "File",
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"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/dbsnp_137.b37.vcf"
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"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/dbsnp_137.b37.vcf",
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},
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"cosmic": {
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"class": "File",
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"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/CosmicCodingMuts_v67_b37_20131024__NDS.vcf"
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"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/CosmicCodingMuts_v67_b37_20131024__NDS.vcf",
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},
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"ref_fasta": {
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"class": "File",
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"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/v20221027_viral_updates/hg19_virus.fa"
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"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/v20221027_viral_updates/hg19_virus.fa",
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},
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"exac_filter": {
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"class": "File",
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"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz"
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"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz",
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},
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"hotspots": {
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"class": "File",
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"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/hotspot-list-union-v1-v2.txt"
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"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/hotspot-list-union-v1-v2.txt",
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},
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"blacklist_file": {
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"class": "File",
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"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/ACCESS_blacklist_20_05_2019.txt"
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"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/ACCESS_blacklist_20_05_2019.txt",
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},
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"heme_hotspots": {
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"class": "File",
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"path": "iris:///usersoftware/core005/accessH/development/access_heme/resources/access_data/variant_calling/Hv1/ACCESSH_hotspots.txt",
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},
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"heme_tsgs": {
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"class": "File",
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"path": "iris:///usersoftware/core005/accessH/development/access_heme/resources/access_data/variant_calling/Hv1/ACCESSH_TSGs.txt",
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},
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"custom_enst_file": {
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"class": "File",
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"location": "iris:///usersoftware/core005/accessH/development/access_heme/resources/access_data/variant_calling/Hv1/dmp_isoform_merged_overrides.txt"
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"location": "iris:///usersoftware/core005/accessH/development/access_heme/resources/access_data/variant_calling/Hv1/dmp_isoform_merged_overrides.txt",
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},
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"bed_file": {
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"class": "File",
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"location": "iris:///usersoftware/core005/accessH/development/access_heme/resources/access_data/variant_calling/Hv1/MSK-ACCESS-Heme-v1_canonicaltargets_500buffer.bed"
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"location": "iris:///usersoftware/core005/accessH/development/access_heme/resources/access_data/variant_calling/Hv1/MSK-ACCESS-Heme-v1_canonicaltargets_500buffer.bed",
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},
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"annotate_concat_header_file": {
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"class": "File",
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"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/mutect_annotate_concat_header.txt"
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"location": "iris:///data1/core006/accessH/production/resources/ACCESS-data/mutect_annotate_concat_header.txt",
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},
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"reference_bam_for_VC": {
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"class": "File",
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"location": "iris:///data1/core006/accessH/production/resources/Hv1/reference_bam_for_unmatched_VC/Donor3F41c2207-TPH01_ACCESSHv1-VAL-20220007_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam"
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"location": "iris:///data1/core006/accessH/production/resources/Hv1/reference_bam_for_unmatched_VC/Donor3F41c2207-TPH01_ACCESSHv1-VAL-20220007_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam",
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},
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"reference_bam_for_SV": {
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"class": "File",
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"location": "iris:///data1/core006/accessH/production/resources/Hv1/reference_bam_for_SV/Donor3F41c2207-TPH01_ACCESSHv1-VAL-20220007_cl_aln_srt_MD_IR_FX_BR.bam"
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"location": "iris:///data1/core006/accessH/production/resources/Hv1/reference_bam_for_SV/Donor3F41c2207-TPH01_ACCESSHv1-VAL-20220007_cl_aln_srt_MD_IR_FX_BR.bam",
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},
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"run_tools": {
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"bcftools": "/usersoftware/core005/access/production/V1/tools/bcftools-1.9/bcftools",
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"gbcms": "/usersoftware/core005/access/production/V1/tools/GetBaseCountsMultiSample-1.2.5/GetBaseCountsMultiSample",
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"java_7": "/admin/software/migration-testing/java/jdk1.7.0_80/bin/java",
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"mutect": "/usersoftware/core005/access/production/V1/tools/muTect/versions/v1.1.5/muTect-1.1.5.jar",
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"vardict": "/usersoftware/core005/access/production/V1/tools/vardict/v1.5.1/bin/VarDict",
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"vardict_testsomatic": "/usersoftware/core005/access/production/V1/tools/vardict/v1.5.1/vardict_328e00a/testsomatic.R",
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"vardict_var2vcf_paired": "/usersoftware/core005/access/production/V1/tools/vardict/v1.5.1/vardict_328e00a/var2vcf_paired.pl",
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"perl": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin/perl",
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"vcf2maf": "/usersoftware/core005/access/production/V1/tools/vcf2maf/mskcc-vcf2maf-2235eed/vcf2maf.pl",
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"vep_path": "/data1/core005/assets/msk-access/v1.0/vep/v86/",
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"vep_data": "/data1/core005/assets/msk-access/v1.0/vep/cache/",
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"tabix": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin/tabix",
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"bgzip": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin/bgzip",
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"sortbed": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin/sortBed",
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"bcftools_1_6": "/usersoftware/core005/access/production/V1/tools/bcftools-1.9/bcftools"
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}
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"bcftools": "/usersoftware/core005/access/production/V1/tools/bcftools-1.9/bcftools",
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"gbcms": "/usersoftware/core005/access/production/V1/tools/GetBaseCountsMultiSample-1.2.5/GetBaseCountsMultiSample",
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"java_7": "/admin/software/migration-testing/java/jdk1.7.0_80/bin/java",
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"mutect": "/usersoftware/core005/access/production/V1/tools/muTect/versions/v1.1.5/muTect-1.1.5.jar",
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"vardict": "/usersoftware/core005/access/production/V1/tools/vardict/v1.5.1/bin/VarDict",
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"vardict_testsomatic": "/usersoftware/core005/access/production/V1/tools/vardict/v1.5.1/vardict_328e00a/testsomatic.R",
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"vardict_var2vcf_paired": "/usersoftware/core005/access/production/V1/tools/vardict/v1.5.1/vardict_328e00a/var2vcf_paired.pl",
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"perl": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin/perl",
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"vcf2maf": "/usersoftware/core005/access/production/V1/tools/vcf2maf/mskcc-vcf2maf-2235eed/vcf2maf.pl",
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"vep_path": "/data1/core005/assets/msk-access/v1.0/vep/v86/",
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"vep_data": "/data1/core005/assets/msk-access/v1.0/vep/cache/",
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"tabix": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin/tabix",
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"bgzip": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin/bgzip",
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"sortbed": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin/sortBed",
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"bcftools_1_6": "/usersoftware/core005/access/production/V1/tools/bcftools-1.9/bcftools",
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},
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}

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