From e6595467df259d2c4aaaca51efe2a7ac49b9d5fa Mon Sep 17 00:00:00 2001 From: chriscrsmith Date: Tue, 21 Mar 2023 10:45:18 -0700 Subject: [PATCH 1/9] proposed production-level config for humans --- ...duction-config.yml => production_config_HomSap.yml} | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) rename workflows/config/snakemake/{production-config.yml => production_config_HomSap.yml} (71%) diff --git a/workflows/config/snakemake/production-config.yml b/workflows/config/snakemake/production_config_HomSap.yml similarity index 71% rename from workflows/config/snakemake/production-config.yml rename to workflows/config/snakemake/production_config_HomSap.yml index 71fc962c..4da47e15 100644 --- a/workflows/config/snakemake/production-config.yml +++ b/workflows/config/snakemake/production_config_HomSap.yml @@ -1,7 +1,6 @@ "seed": 12345 "population_id": 0 -"num_samples_per_population": [10, 10, 10] -"replicates": 20 +"replicates": 3 "species": "HomSap" "demo_models": [ @@ -11,9 +10,12 @@ {"id":"OutOfAfrica_3G09", "num_samples_per_population": [100,100,100], } + {"id":"OutOfAfricaArchaicAdmixture_5R19", + "num_samples_per_population": [100,100,100], + } ] "genetic_map": "HapMapII_GRCh37" -"chrm_list": "chr21" +"chrm_list": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21" "dfe_list": ["Gamma_H17"] "annotation_list": ["all_sites", "ensembl_havana_104_exons"] "output_dir": "results" @@ -31,6 +33,6 @@ # exe paths "poly_dfe_exec": "ext/polyDFE/polyDFE-2.0-linux-64-bit" "dfe_alpha_data_path_1": "ext/DFE-alpha/data" -"dfe_alpha_data_path_2": "three-epoch" +"dfe_alpha_data_path_2": "three-epoch" "msmc_exec" : "ext/msmc2/build/release/msmc2" "stairwayplot_code" : "stairwayplot/swarmops.jar" From fd69e35fb9487a1fed0aba5d70e294dab1a99829 Mon Sep 17 00:00:00 2001 From: Chris Smith Date: Tue, 21 Mar 2023 10:53:28 -0700 Subject: [PATCH 2/9] Update production_config_HomSap.yml --- workflows/config/snakemake/production_config_HomSap.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/config/snakemake/production_config_HomSap.yml b/workflows/config/snakemake/production_config_HomSap.yml index 4da47e15..a2990e91 100644 --- a/workflows/config/snakemake/production_config_HomSap.yml +++ b/workflows/config/snakemake/production_config_HomSap.yml @@ -15,7 +15,7 @@ } ] "genetic_map": "HapMapII_GRCh37" -"chrm_list": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21" +"chrm_list": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22" "dfe_list": ["Gamma_H17"] "annotation_list": ["all_sites", "ensembl_havana_104_exons"] "output_dir": "results" From 21c2b57c8d4f6e4978f02011be7604cd9edfc891 Mon Sep 17 00:00:00 2001 From: chriscrsmith Date: Wed, 29 Mar 2023 18:10:09 -0700 Subject: [PATCH 3/9] scotts suggestions --- .../snakemake/production_config_HomSap.yml | 37 ++++++++++++++----- 1 file changed, 27 insertions(+), 10 deletions(-) diff --git a/workflows/config/snakemake/production_config_HomSap.yml b/workflows/config/snakemake/production_config_HomSap.yml index 4da47e15..9ca05222 100644 --- a/workflows/config/snakemake/production_config_HomSap.yml +++ b/workflows/config/snakemake/production_config_HomSap.yml @@ -1,7 +1,11 @@ +"population_id": [0] # (what is this a setting for?) + +# snakemake settings "seed": 12345 -"population_id": 0 "replicates": 3 +"output_dir": "results" +# species-specific settings "species": "HomSap" "demo_models": [ {"id":"Constant", @@ -16,23 +20,36 @@ ] "genetic_map": "HapMapII_GRCh37" "chrm_list": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21" -"dfe_list": ["Gamma_H17"] +"dfe_list": ["none", "Gamma_H17"] "annotation_list": ["all_sites", "ensembl_havana_104_exons"] -"output_dir": "results" - +"mask_file": "workflows/masks/HapmapII_GRCh37.mask.bed" +"stairway_annot_mask" : "" # set this or any of the below to 'none' to skip annot masking +"msmc_annot_mask" : "" +"gone_annot_mask" : "" +"smcpp_annot_mask" : "" # slim settings "slim_scaling_factor": 1 "slim_burn_in": 10 # n(t) specific configs -"num_sampled_genomes_msmc" : [2, 8] -"num_sampled_genomes_per_replicate": [2, 8] -"num_msmc_iterations" : 1 +"methods" : ["stairwayplot", "gone", "smcpp", "msmc"] +"num_sampled_genomes_msmc" : [6] +"num_sampled_genomes_per_replicate": [2] +"num_msmc_iterations" : 20 +"gone_phase" : 1 # 0 for pseudohaploid, 1 for phased, 2 for unknown phase +"gone_max_snps" : 50000 # default=50000 +"gone_threads" : 8 +"gone_num_gens" : 2000 # default=2000 +"gone_num_bins" : 400 # default=400 + # exe paths "poly_dfe_exec": "ext/polyDFE/polyDFE-2.0-linux-64-bit" -"dfe_alpha_data_path_1": "ext/DFE-alpha/data" -"dfe_alpha_data_path_2": "three-epoch" +"dfe_alpha_exec": "ext/dfe-alpha-release-2.16/est_dfe" +"dfe_alpha_data_path_1": "ext/dfe-alpha-release-2.16/data" +"dfe_alpha_data_path_2": "three-epoch" +"grapes_exec": "ext/grapes/multi_grapes" "msmc_exec" : "ext/msmc2/build/release/msmc2" -"stairwayplot_code" : "stairwayplot/swarmops.jar" +"stairwayplot_code" : "ext/stairwayplot/swarmops.jar" +"gone_code" : "ext/GONE/Linux" From ee5e0d9857c4f7c7dbd8e6482757a230f9a0183b Mon Sep 17 00:00:00 2001 From: chriscrsmith Date: Wed, 29 Mar 2023 18:17:31 -0700 Subject: [PATCH 4/9] modeling after tiny config --- .../snakemake/production_config_HomSap.yml | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 workflows/config/snakemake/production_config_HomSap.yml diff --git a/workflows/config/snakemake/production_config_HomSap.yml b/workflows/config/snakemake/production_config_HomSap.yml new file mode 100644 index 00000000..9ca05222 --- /dev/null +++ b/workflows/config/snakemake/production_config_HomSap.yml @@ -0,0 +1,55 @@ +"population_id": [0] # (what is this a setting for?) + +# snakemake settings +"seed": 12345 +"replicates": 3 +"output_dir": "results" + +# species-specific settings +"species": "HomSap" +"demo_models": [ + {"id":"Constant", + "num_samples_per_population": [100], + }, + {"id":"OutOfAfrica_3G09", + "num_samples_per_population": [100,100,100], + } + {"id":"OutOfAfricaArchaicAdmixture_5R19", + "num_samples_per_population": [100,100,100], + } +] +"genetic_map": "HapMapII_GRCh37" +"chrm_list": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21" +"dfe_list": ["none", "Gamma_H17"] +"annotation_list": ["all_sites", "ensembl_havana_104_exons"] +"mask_file": "workflows/masks/HapmapII_GRCh37.mask.bed" +"stairway_annot_mask" : "" # set this or any of the below to 'none' to skip annot masking +"msmc_annot_mask" : "" +"gone_annot_mask" : "" +"smcpp_annot_mask" : "" + +# slim settings +"slim_scaling_factor": 1 +"slim_burn_in": 10 + +# n(t) specific configs +"methods" : ["stairwayplot", "gone", "smcpp", "msmc"] +"num_sampled_genomes_msmc" : [6] +"num_sampled_genomes_per_replicate": [2] +"num_msmc_iterations" : 20 +"gone_phase" : 1 # 0 for pseudohaploid, 1 for phased, 2 for unknown phase +"gone_max_snps" : 50000 # default=50000 +"gone_threads" : 8 +"gone_num_gens" : 2000 # default=2000 +"gone_num_bins" : 400 # default=400 + + +# exe paths +"poly_dfe_exec": "ext/polyDFE/polyDFE-2.0-linux-64-bit" +"dfe_alpha_exec": "ext/dfe-alpha-release-2.16/est_dfe" +"dfe_alpha_data_path_1": "ext/dfe-alpha-release-2.16/data" +"dfe_alpha_data_path_2": "three-epoch" +"grapes_exec": "ext/grapes/multi_grapes" +"msmc_exec" : "ext/msmc2/build/release/msmc2" +"stairwayplot_code" : "ext/stairwayplot/swarmops.jar" +"gone_code" : "ext/GONE/Linux" From 79bd6dbaa3c534f95118352f74b996b0b597b150 Mon Sep 17 00:00:00 2001 From: chriscrsmith Date: Tue, 4 Apr 2023 11:08:55 -0700 Subject: [PATCH 5/9] using updated genetic map; cleaned up some unused parameters --- workflows/README.md | 10 +------ workflows/config/snakemake/config.yaml | 2 -- .../config/snakemake/gen_unit_tests.yaml | 2 -- .../config/snakemake/neutral-config.yaml | 2 -- .../snakemake/production_config_HomSap.yml | 11 +++----- workflows/config/snakemake/tiny_config.yaml | 2 -- workflows/masks/HapmapII_GRCh38.mask.bed | 28 +++++++++++++++++++ workflows/n_t.snake | 5 ---- workflows/test/config.json | 3 -- 9 files changed, 33 insertions(+), 32 deletions(-) create mode 100644 workflows/masks/HapmapII_GRCh38.mask.bed diff --git a/workflows/README.md b/workflows/README.md index 4191e007..9228c613 100644 --- a/workflows/README.md +++ b/workflows/README.md @@ -39,10 +39,8 @@ might look like this: ```json { "seed" : 12345, - "population_id" : 0, "num_samples_per_population" : [20, 0, 0], "num_sampled_genomes_msmc" : "2,8", - "num_sampled_genomes_per_replicate": "2,8", "num_msmc_iterations" : 20, "replicates" : 1, "species" : "HomSap", @@ -115,9 +113,6 @@ with selection being 'none', 'all' or applied to the 'exons'. This sets the seed such that any analysis configuration and run can be replicated exactly. -`population_id` : `` -This specifies which population will be plotted. - `num_sampled_genomes_per_population` : `` This is the haploid number of genomes to simulate for an analysis run per population. @@ -129,10 +124,7 @@ analyze. This variable allows the user to run msmc independently on multiple sample sizes (to be specified as a comma-separated string of sample sizes). For each of these sample sizes, -`replicates` number of analyses will be run with `msmc`. All of these numbers should -not exceed `num_sampled_genomes_per_replicate` because the input files are -generated by pruning the tree sequences from the original simulations. -(We might want to do this for the other two programs, as well?) +`replicates` number of analyses will be run with `msmc`. `num_msmc_iterations` : `` The number of iterations for each `msmc` run diff --git a/workflows/config/snakemake/config.yaml b/workflows/config/snakemake/config.yaml index 35e522e0..f9633345 100644 --- a/workflows/config/snakemake/config.yaml +++ b/workflows/config/snakemake/config.yaml @@ -1,5 +1,4 @@ "seed": 12345 -"population_id": 0 "num_samples_per_population": [10, 10, 10] "replicates": 3 @@ -30,7 +29,6 @@ # n(t) specific configs "num_sampled_genomes_msmc": [2] -"num_sampled_genomes_per_replicate": [2] "num_msmc_iterations": 3 "annotation_list": ["ensembl_havana_104_exons"] diff --git a/workflows/config/snakemake/gen_unit_tests.yaml b/workflows/config/snakemake/gen_unit_tests.yaml index a95974e5..4a769cfc 100644 --- a/workflows/config/snakemake/gen_unit_tests.yaml +++ b/workflows/config/snakemake/gen_unit_tests.yaml @@ -1,5 +1,4 @@ "seed": 12345 -"population_id": 0 "replicates": 3 "species": "HomSap" @@ -37,7 +36,6 @@ "methods" : ["stairwayplot", "gone", "smcpp", "msmc"] "num_sampled_genomes_msmc" : [2, 4] -"num_sampled_genomes_per_replicate": [2] # I dont use this, not sure what is purpose? "num_msmc_iterations" : 10 "gone_phase" : 1 # 0 for pseudohaploid, 1 for phased, 2 for unknown phase diff --git a/workflows/config/snakemake/neutral-config.yaml b/workflows/config/snakemake/neutral-config.yaml index 96bbbe4d..2309e618 100644 --- a/workflows/config/snakemake/neutral-config.yaml +++ b/workflows/config/snakemake/neutral-config.yaml @@ -1,5 +1,4 @@ "seed": 12345 -"population_id": 0 "replicates": 3 "species": "HomSap" @@ -29,7 +28,6 @@ # n(t) specific configs "num_sampled_genomes_msmc": [2] -"num_sampled_genomes_per_replicate": [2] "num_msmc_iterations": 3 "annotation_list": ["none"] diff --git a/workflows/config/snakemake/production_config_HomSap.yml b/workflows/config/snakemake/production_config_HomSap.yml index 9ca05222..4d0bf737 100644 --- a/workflows/config/snakemake/production_config_HomSap.yml +++ b/workflows/config/snakemake/production_config_HomSap.yml @@ -1,5 +1,3 @@ -"population_id": [0] # (what is this a setting for?) - # snakemake settings "seed": 12345 "replicates": 3 @@ -12,17 +10,17 @@ "num_samples_per_population": [100], }, {"id":"OutOfAfrica_3G09", - "num_samples_per_population": [100,100,100], + "num_samples_per_population": 3*[100], # shared 'n'; order of pops unclear } {"id":"OutOfAfricaArchaicAdmixture_5R19", - "num_samples_per_population": [100,100,100], + "num_samples_per_population": 3*[100], } ] -"genetic_map": "HapMapII_GRCh37" +"genetic_map": "HapMapII_GRCh38" "chrm_list": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21" "dfe_list": ["none", "Gamma_H17"] "annotation_list": ["all_sites", "ensembl_havana_104_exons"] -"mask_file": "workflows/masks/HapmapII_GRCh37.mask.bed" +"mask_file": "workflows/masks/HapmapII_GRCh38.mask.bed" "stairway_annot_mask" : "" # set this or any of the below to 'none' to skip annot masking "msmc_annot_mask" : "" "gone_annot_mask" : "" @@ -35,7 +33,6 @@ # n(t) specific configs "methods" : ["stairwayplot", "gone", "smcpp", "msmc"] "num_sampled_genomes_msmc" : [6] -"num_sampled_genomes_per_replicate": [2] "num_msmc_iterations" : 20 "gone_phase" : 1 # 0 for pseudohaploid, 1 for phased, 2 for unknown phase "gone_max_snps" : 50000 # default=50000 diff --git a/workflows/config/snakemake/tiny_config.yaml b/workflows/config/snakemake/tiny_config.yaml index d3322c11..4e22f70c 100644 --- a/workflows/config/snakemake/tiny_config.yaml +++ b/workflows/config/snakemake/tiny_config.yaml @@ -1,5 +1,4 @@ "seed": 12345 -"population_id": [0] "replicates": 2 "species": "HomSap" @@ -31,7 +30,6 @@ "methods" : ["stairwayplot", "gone", "smcpp", "msmc"] "num_sampled_genomes_msmc" : [6] -"num_sampled_genomes_per_replicate": [2] # I dont use this, not sure what is purpose? "num_msmc_iterations" : 20 "gone_phase" : 1 # 0 for pseudohaploid, 1 for phased, 2 for unknown phase diff --git a/workflows/masks/HapmapII_GRCh38.mask.bed b/workflows/masks/HapmapII_GRCh38.mask.bed new file mode 100644 index 00000000..bdae41b0 --- /dev/null +++ b/workflows/masks/HapmapII_GRCh38.mask.bed @@ -0,0 +1,28 @@ +chr10 38861078 41705569 +chr1 121569984 143276353 +chr11 50795892 54555633 +chr12 34700914 37463389 +chr13 1 18447064 +chr14 1 19198131 +chr15 1 19809716 +chr16 36034945 46428208 +chr17 22738887 26950488 +chr18 15409995 20934306 +chr19 24373307 27244449 +chr20 26328611 30187700 +chr21 10646501 12968298 +chr21 1 10326653 +chr22 1 15287921 +chr2 90236658 91433610 +chr2 92117097 94663732 +chr3 90427071 93808853 +chr4 49627542 51818712 +chr5 46363876 50291681 +chr6 58452161 60342543 +chr7 57870656 61072218 +chr8 43936537 46006821 +chr9 38743712 40906821 +chr9 41438036 62926704 +chr9 66183582 68223187 +chrX 1 2785350 +chrX 58456814 62611346 diff --git a/workflows/n_t.snake b/workflows/n_t.snake index b29413a1..aeb509c8 100644 --- a/workflows/n_t.snake +++ b/workflows/n_t.snake @@ -23,7 +23,6 @@ import gone import plots import masks -# TODO: Add support for population_id list, right now it runs on all pops # TODO: add support for running some but not all inference methods # NOTE: see other todo specific to rule below # ############################################################################### @@ -42,8 +41,6 @@ species = stdpopsim.get_species(config["species"]) # This is the number of samples to simulate for within each population # for each replicate -# TODO double check this is up to date with stdpopsim backend -population_id = config["population_id"] # Here is a list of sample sizes to run msmc on. # Each element counts as its own analysis @@ -54,7 +51,6 @@ num_sampled_genomes_msmc = config["num_sampled_genomes_msmc"] # typically 20 num_msmc_iterations = config["num_msmc_iterations"] -num_sampled_genomes_per_replicate = config["num_sampled_genomes_per_replicate"] # The number of replicates of each analysis you would like to run # For now leaving it a 1 just to get results quickly @@ -309,7 +305,6 @@ rule plot_compound_stairway: # TODO: ln 379, get wildcards.samps to work so that num_sampled_genomes_msmc are run in parallel # sample size num_sampled_genomes_msmc = config["num_sampled_genomes_msmc"] -num_sampled_genomes_per_replicate = config["num_sampled_genomes_per_replicate"] # The number of msmc Baumwelch iterations to run num_msmc_iterations = config["num_msmc_iterations"] msmc_exec = config["msmc_exec"] diff --git a/workflows/test/config.json b/workflows/test/config.json index 76ab7a43..267d8f4b 100755 --- a/workflows/test/config.json +++ b/workflows/test/config.json @@ -1,5 +1,4 @@ "seed": 12345 -"population_id": 0 "num_samples_per_population": [10, 0, 0] "replicates": 2 "species": "HomSap" @@ -10,7 +9,5 @@ "dfe_list": ["Gamma_H17"] "output_dir": "results" "poly_dfe_exec": "../ext/polyDFE/polyDFE-2.0-linux-64-bit" -"num_sampled_genomes_msmc" : "2,8" -"num_sampled_genomes_per_replicate": "2,8" "num_msmc_iterations" : 20 "slim_scaling_factor": 10 From 1ad00dc4cb5f8d7b794b4c2d4d5c5fc85760e3cb Mon Sep 17 00:00:00 2001 From: Chris Smith Date: Wed, 12 Apr 2023 14:21:52 -0700 Subject: [PATCH 6/9] Update production_config_HomSap.yml --- workflows/config/snakemake/production_config_HomSap.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/config/snakemake/production_config_HomSap.yml b/workflows/config/snakemake/production_config_HomSap.yml index 4d0bf737..48669e55 100644 --- a/workflows/config/snakemake/production_config_HomSap.yml +++ b/workflows/config/snakemake/production_config_HomSap.yml @@ -18,8 +18,8 @@ ] "genetic_map": "HapMapII_GRCh38" "chrm_list": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21" -"dfe_list": ["none", "Gamma_H17"] -"annotation_list": ["all_sites", "ensembl_havana_104_exons"] +"dfe_list": ["none", "Gamma_H17", "Gamma_K17"] +"annotation_list": ["all_sites", "ensembl_havana_104_exons", "ensembl_havana_104_exons"] "mask_file": "workflows/masks/HapmapII_GRCh38.mask.bed" "stairway_annot_mask" : "" # set this or any of the below to 'none' to skip annot masking "msmc_annot_mask" : "" From 4aa63f2cf06b4760d6cc0db0caebfedf1194e00d Mon Sep 17 00:00:00 2001 From: Chris Smith Date: Wed, 12 Apr 2023 14:22:34 -0700 Subject: [PATCH 7/9] Update production_config_HomSap.yml --- workflows/config/snakemake/production_config_HomSap.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/config/snakemake/production_config_HomSap.yml b/workflows/config/snakemake/production_config_HomSap.yml index 48669e55..4fc03294 100644 --- a/workflows/config/snakemake/production_config_HomSap.yml +++ b/workflows/config/snakemake/production_config_HomSap.yml @@ -17,7 +17,7 @@ } ] "genetic_map": "HapMapII_GRCh38" -"chrm_list": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21" +"chrm_list": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22" "dfe_list": ["none", "Gamma_H17", "Gamma_K17"] "annotation_list": ["all_sites", "ensembl_havana_104_exons", "ensembl_havana_104_exons"] "mask_file": "workflows/masks/HapmapII_GRCh38.mask.bed" From 12e5f970bd02a69cfbbfcf23cd303a7a9f333494 Mon Sep 17 00:00:00 2001 From: Chris Smith Date: Thu, 13 Apr 2023 08:54:54 -0700 Subject: [PATCH 8/9] Update production_config_HomSap.yml --- workflows/config/snakemake/production_config_HomSap.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/workflows/config/snakemake/production_config_HomSap.yml b/workflows/config/snakemake/production_config_HomSap.yml index 4fc03294..82a00714 100644 --- a/workflows/config/snakemake/production_config_HomSap.yml +++ b/workflows/config/snakemake/production_config_HomSap.yml @@ -9,9 +9,6 @@ {"id":"Constant", "num_samples_per_population": [100], }, - {"id":"OutOfAfrica_3G09", - "num_samples_per_population": 3*[100], # shared 'n'; order of pops unclear - } {"id":"OutOfAfricaArchaicAdmixture_5R19", "num_samples_per_population": 3*[100], } From 1e61a6e5d415896b3d077dfb4fe14ec68468cc99 Mon Sep 17 00:00:00 2001 From: Chris Smith Date: Tue, 26 Sep 2023 09:37:01 -0700 Subject: [PATCH 9/9] down to a single DFE model --- workflows/config/snakemake/production_config_HomSap.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/config/snakemake/production_config_HomSap.yml b/workflows/config/snakemake/production_config_HomSap.yml index 82a00714..21b0d098 100644 --- a/workflows/config/snakemake/production_config_HomSap.yml +++ b/workflows/config/snakemake/production_config_HomSap.yml @@ -15,7 +15,7 @@ ] "genetic_map": "HapMapII_GRCh38" "chrm_list": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22" -"dfe_list": ["none", "Gamma_H17", "Gamma_K17"] +"dfe_list": ["none", "Gamma_K17"] "annotation_list": ["all_sites", "ensembl_havana_104_exons", "ensembl_havana_104_exons"] "mask_file": "workflows/masks/HapmapII_GRCh38.mask.bed" "stairway_annot_mask" : "" # set this or any of the below to 'none' to skip annot masking