fixed bug in location of fusion STAR libraries

CCBR · Oct 9, 2018 · ce76291 · ce76291
1 parent fa5b8b5
commit ce76291
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/hg19.json b/hg19.json
@@ -167,7 +167,7 @@
 #    "SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/human_gencode.transcripts.fa",
     "STARREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/Star_refs/hs37d5/genes-",
 #    "RRNALIST2": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5/annotation/gencode.v19.annotation.gtf.rRNA.interval_list",
-    "STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh37_gencode_v19_CTAT_lib_July272016_prebuilt",
+    "STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir",
     "FUSCATCHDAT": "/usr/local/apps/fusioncatcher/1.00/fusioncatcher/data/human_v90",
     "FUSCATCHCONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_hg38_configuration.cfg",
     "FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",

diff --git a/hg38.json b/hg38.json
@@ -58,8 +58,8 @@
     "MUTECTVARIANTS": "--dbsnp /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz --cosmic /data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz",
     "VEPBUILD": "GRCh38",
     "VEPSPECIES": "homo_sapiens",
-    "VEPFILTERVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/ExAC_nonTCGA.r1.sites.hg38.vep.vcf.gz",
-    "VEPGENOME": "/fdb/VEP/88/cache/GRCh38.fa",
+    "VEPFILTERVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/ExAC_nonTCGA.r0.3.1.sites.vep.GRCh38.vcf.gz",
+    "VEPGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
     "CANVASGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/GRCh38/WholeGenomeFasta",
     "CANVASKMER": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/GRCh38/kmer.fa",
     "CANVASFILTER": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/GRCh38/filter13.bed",
@@ -127,8 +127,8 @@
     "MUTECTVARIANTS": "--dbsnp /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz --cosmic /data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz",
     "VEPBUILD": "GRCh38",
     "VEPSPECIES": "homo_sapiens",
-    "VEPFILTERVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/ExAC_nonTCGA.r1.sites.hg38.vep.vcf.gz",
-    "VEPGENOME": "/fdb/VEP/88/cache/GRCh38.fa",
+    "VEPFILTERVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/ExAC_nonTCGA.r0.3.1.sites.vep.GRCh38.vcf.gz",
+    "VEPGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
     "CANVASGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/GRCh38/WholeGenomeFasta",
     "CANVASPLOIDY": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_knownPloidy_hg19.vcf",
     "CANVASKMER": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/GRCh38/kmer.fa",
@@ -159,7 +159,7 @@
      "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
      "STARREF": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_human/release_26/genes-",
 #     "RRNALIST2": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg38.rRNA.interval_list_R26",
-    "STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38_gencode_v24_CTAT_lib_Mar292017_prebuilt",
+    "STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir",
     "FUSCATCHDAT": "/usr/local/apps/fusioncatcher/1.00/fusioncatcher/data/human_v90",
     "FUSCATCHCONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_hg38_configuration.cfg",
     "GENOME": "/fdb/GENCODE/Gencode_human/release_26/GRCh38.primary_assembly.genome.fa",