Merge pull request #430 from jlac/activeDev

update hg38 PON
CCBR · Sep 30, 2019 · 6dccc34 · 6dccc34
2 parents 963b73f + b922e97
commit 6dccc34
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/Rules/all-wgs-somatic.rl b/Rules/all-wgs-somatic.rl
@@ -15,7 +15,7 @@ if config['project']['annotation'] == "hg19":
             config['project']['workpath']+"/mutect2_out",
             config['project']['workpath']+"/mutect_out",
             expand(config['project']['workpath']+"/conpair_out/{p}.conpair", p=pairs),
-            "sample_network.bmp",
+            "sample_network_mqc.png",
             config['project']['workpath']+"/mutect2_out/mutect2_variants.database",
             config['project']['workpath']+"/mutect_out/mutect_variants.database",
             config['project']['workpath']+"/strelka_out/strelka_variants.database",
@@ -55,7 +55,7 @@ elif config['project']['annotation'] == "hg38":
             config['project']['workpath']+"/mutect2_out",
             config['project']['workpath']+"/mutect_out",
             expand(config['project']['workpath']+"/conpair_out/{p}.conpair", p=pairs),
-            "sample_network.bmp",
+            "sample_network_mqc.png",
             config['project']['workpath']+"/mutect2_out/mutect2_variants.database",
             config['project']['workpath']+"/mutect_out/mutect_variants.database",
             config['project']['workpath']+"/strelka_out/strelka_variants.database",
@@ -96,7 +96,7 @@ elif config['project']['annotation'] == "mm10":
             config['project']['workpath']+"/mutect2_out/mutect2_variants.database",
             config['project']['workpath']+"/mutect_out/mutect_variants.database",
             config['project']['workpath']+"/strelka_out/strelka_variants.database",
-            "sample_network.bmp",
+            "sample_network_mqc.png",
             config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_variants.maf",
             config['project']['workpath']+"/mutect2_out/mutsigCV_out/somatic.sig_genes.txt",
             config['project']['workpath']+"/strelka_out/oncotator_out/strelka_variants.maf",

diff --git a/hg38.json b/hg38.json
@@ -2,7 +2,7 @@
     "exomeseq": {
     "VARDICTBED": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.chroms.bed",
     "BWAGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
-    "PON": "/data/CCBR_Pipeliner/db/PipeDB/lib/1kGenomes_ExAC_0.001freq_PON.hg38.vcf.gz",
+    "PON": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38.noCOSMIC_ClinVar.pon.vcf.gz",
     "GENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
     "CNVKITGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
 #    "CNVKITREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1_flatRef.cnn",
@@ -77,7 +77,7 @@
     "genomeseq": {
     "VARDICTBED": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.chroms.bed",
     "BWAGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
-    "PON": "/data/CCBR_Pipeliner/db/PipeDB/lib/1kGenomes_ExAC_0.001freq_PON.hg38.vcf.gz",
+    "PON": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38.noCOSMIC_ClinVar.pon.vcf.gz",
     "GENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
     "CNVKITGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
     "CNVKITREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1_flatRef.cnn",