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b/example/imputation.snplist new file mode 100644 index 00000000..231104ce --- /dev/null +++ b/example/imputation.snplist @@ -0,0 +1,100 @@ +var0 +var1 +var2 +var3 +var4 +var5 +var6 +var7 +var8 +var9 +var10 +var11 +var12 +var13 +var14 +var15 +var16 +var17 +var18 +var19 +var20 +var21 +var22 +var23 +var24 +var25 +var26 +var27 +var28 +var29 +var30 +var31 +var32 +var33 +var34 +var35 +var36 +var37 +var38 +var39 +var40 +var41 +var42 +var43 +var44 +var45 +var46 +var47 +var48 +var49 +var50 +var51 +var52 +var53 +var54 +var55 +var56 +var57 +var58 +var59 +var60 +var61 +var62 +var63 +var64 +var65 +var66 +var67 +var68 +var69 +var70 +var71 +var72 +var73 +var74 +var75 +var76 +var77 +var78 +var79 +var80 +var81 +var82 +var83 +var84 +var85 +var86 +var87 +var88 +var89 +var90 +var91 +var92 +var93 +var94 +var95 +var96 +var97 +var98 +var99 diff --git a/example/preprocess/data/vcf/test_vcf_data_c21_b1.vcf.gz b/example/preprocess/data/vcf/test_vcf_data_c21_b1.vcf.gz index df2edae1..a23f74b6 100644 Binary files a/example/preprocess/data/vcf/test_vcf_data_c21_b1.vcf.gz and b/example/preprocess/data/vcf/test_vcf_data_c21_b1.vcf.gz differ diff --git a/example/preprocess/data/vcf/test_vcf_data_c22_b1.vcf.gz b/example/preprocess/data/vcf/test_vcf_data_c22_b1.vcf.gz index 6228dc90..4853b986 100644 Binary files a/example/preprocess/data/vcf/test_vcf_data_c22_b1.vcf.gz and b/example/preprocess/data/vcf/test_vcf_data_c22_b1.vcf.gz differ diff --git a/pipelines/association_testing/regress_eval_regenie.snakefile b/pipelines/association_testing/regress_eval_regenie.snakefile index 78c26a10..507fabaf 100644 --- a/pipelines/association_testing/regress_eval_regenie.snakefile +++ b/pipelines/association_testing/regress_eval_regenie.snakefile @@ -19,7 +19,10 @@ regenie_step2_bsize = regenie_config_step2["bsize"] regenie_njobs = regenie_config_step1.get("njobs", 1) regenie_joblist = range(1, regenie_njobs) - +cv_exp = config.get("cv_exp", False) +config_file_prefix = ( + "cv_split0/deeprvat/" if cv_exp else "" +) wildcard_constraints: job="\d+" diff --git a/pipelines/association_testing_precomputed_burdens_regenie.snakefile b/pipelines/association_testing_precomputed_burdens_regenie.snakefile index 9eac0f43..b6778b05 100644 --- a/pipelines/association_testing_precomputed_burdens_regenie.snakefile +++ b/pipelines/association_testing_precomputed_burdens_regenie.snakefile @@ -7,7 +7,7 @@ phenotypes = config['phenotypes'] phenotypes = list(phenotypes.keys()) if type(phenotypes) == dict else phenotypes n_burden_chunks = config.get('n_burden_chunks', 1) if not debug_flag else 2 -n_regression_chunks = config.get('n_regression_chunks', 40) if not debug_flag else 2 +n_avg_chunks = config.get('n_avg_chunks', 40) n_bags = config['training']['n_bags'] if not debug_flag else 3 n_repeats = config['n_repeats'] debug = '--debug ' if debug_flag else '' @@ -19,9 +19,9 @@ wildcard_constraints: trial="\d+", include: "association_testing/config.snakefile" -include: "association_testing/association_dataset_precomputed_burdens.snakefile" +include: "association_testing/association_dataset.snakefile" +include: "association_testing/burdens.snakefile" include: "association_testing/regress_eval_regenie.snakefile" -include: "association_testing/eval.snakefile" rule all: input: