repaired wgs_tumor_only bug in maftools

CCBR · Oct 23, 2018 · 94fa796 · 94fa796
1 parent fa07df2
commit 94fa796
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/Rules/all-wgs-somatic-tumoronly.rl b/Rules/all-wgs-somatic-tumoronly.rl
@@ -13,7 +13,7 @@ if config['project']['annotation'] == "hg19":
 #            config['project']['workpath']+"/cnvkit_out/CNVkit_summary_heatmap.pdf",
             config['project']['workpath']+"/sample_network.bmp",
             config['project']['workpath']+"/mutect2_out/mutect2_variants.database",
-            config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_filtered.maf",
+            config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_variants.maf",
             config['project']['workpath']+"/mutect2_out/mutsigCV_out/somatic.sig_genes.txt",
             expand("manta_out/{s}/results/variants/candidateSV.vcf.gz", s=samples),
             "admixture_out/admixture_table.tsv",
@@ -39,7 +39,7 @@ elif config['project']['annotation'] == "hg38":
 #            config['project']['workpath']+"/cnvkit_out/CNVkit_summary_heatmap.pdf",
             config['project']['workpath']+"/sample_network.bmp",
             config['project']['workpath']+"/mutect2_out/mutect2_variants.database",
-            config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_filtered.maf",
+            config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_variants.maf",
             config['project']['workpath']+"/mutect2_out/mutsigCV_out/somatic.sig_genes.txt",
             expand("manta_out/{s}/results/variants/candidateSV.vcf.gz", s=samples),
             "admixture_out/admixture_table.tsv",
@@ -64,7 +64,7 @@ elif config['project']['annotation'] == "mm10":
 #            config['project']['workpath']+"/cnvkit_out/CNVkit_summary_heatmap.pdf",
             config['project']['workpath']+"/mutect2_out/mutect2_variants.database",
             config['project']['workpath']+"/sample_network.bmp",
-            config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_filtered.maf",
+            config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_variants.maf",
             config['project']['workpath']+"/mutect2_out/mutsigCV_out/somatic.sig_genes.txt",
             expand("manta_out/{s}/results/variants/candidateSV.vcf.gz", s=samples),
             "admixture_out/admixture_table.tsv",