Merge branch 'master' of github.com:jrflab/modules

Author: raylim

b37.inc

@@ -54,11 +54,11 @@ DBSNP ?= $(REF_DIR)/dbsnp_138.b37.gmaf.vcf.gz
 KNOWN_INDELS ?= $(REF_DIR)/GATK_bundle/2.3/Mills_and_1000G_gold_standard.indels.b37.vcf.gz
 OMNI ?= $(REF_DIR)/GATK_bundle/2.3/1000G_omni2.5.b37.vcf.gz
 HAPMAP ?= $(REF_DIR)/GATK_bundle/2.3/hapmap_3.3.b37.vcf.gz
-COSMIC ?= $(REF_DIR)/cosmic_v81/CosmicCodingMuts.vcf.gz
-COSMIC_NONCODING ?= $(REF_DIR)/cosmic_v81/CosmicCodingMuts.vcf.gz
+COSMIC ?= $(REF_DIR)/cosmic_v82/CosmicCodingMuts.vcf.gz
+COSMIC_NONCODING ?= $(REF_DIR)/cosmic_v82/CosmicNonCodingVariants.vcf.gz
 HAPMAP_POP_FILE ?= $(REF_DIR)/b37_gatk_bundle_2017-04-26/hapmap_3.3_b37_pop_stratified_af.vcf.gz
 BOWTIE_REF = $(REF_DIR)/GATK_bundle/2.3/human_g1k_v37
-EXOME_BED ?= $(REF_DIR)/target_panels/sure_select_exome_v3_v4.b37.bed
+EXOME_BED ?= $(REF_DIR)/target_panels/sure_select_exome_v4_b37.bed
 MAP_BIGWIG ?= $(REF_DIR)/wgEncodeCrgMapabilityAlign100mer.nochr.bigWig
 
 EXOME ?= false

hg19.inc

@@ -39,8 +39,8 @@ GISTIC_REF ?= $(HOME)/share/usr/gistic_2_0_21/refgenefiles/hg19.mat
 CLINVAR ?= $(REF_DIR)/clinvar_20160531.hg19.vcf.gz
 EXAC_NONTCGA ?= $(REF_DIR)/ExAC.r0.3.nonTCGA.sites.vep.2.hg19.vcf.gz
 
-COSMIC ?= $(REF_DIR)/cosmic_v81/CosmicCodingMuts.hg19.vcf.gz
-COSMIC_NONCODING ?= $(REF_DIR)/cosmic_v81/CosmicNonCodingVariants.hg19.vcf.gz
+COSMIC ?= $(REF_DIR)/cosmic_v82/CosmicCodingMuts.hg19.vcf.gz
+COSMIC_NONCODING ?= $(REF_DIR)/cosmic_v82/CosmicNonCodingVariants.hg19.vcf.gz
 
 REF_FASTA ?= $(REF_DIR)/ucsc_gatk_bundle_2.8/ucsc.hg19.fasta
 NOCHR_REF_FASTA ?= $(REF_DIR)/GATK_bundle/2.3/human_g1k_v37.fasta
@@ -49,7 +49,7 @@ DBSNP ?= $(REF_DIR)/ucsc_gatk_bundle_2.8/dbsnp_138.hg19.vcf.gz
 KNOWN_INDELS ?= $(REF_DIR)/ucsc_gatk_bundle_2.8/Mills_and_1000G_gold_standard.indels.hg19.vcf.gz
 OMNI ?= $(REF_DIR)/ucsc_gatk_bundle_2.8/1000G_omni2.5.hg19.vcf.gz
 HAPMAP ?= $(REF_DIR)/ucsc_gatk_bundle_2.8/hapmap_3.3.hg19.vcf.gz
-EXOME_BED ?= $(REF_DIR)/target_panels/sure_select_exome_v3_v4.hg19.bed
+EXOME_BED ?= $(REF_DIR)/target_panels/sure_select_exome_v4_hg19.bed
 MAP_BIGWIG ?= $(REF_DIR)/wgEncodeCrgMapabilityAlign100mer.bigWig
 
 EXOME ?= false

summary/mutation_summary_excel.py

@@ -209,7 +209,7 @@ def write_mutation_summary(snps_high_moderate, snps_low_modifier,
         config = yaml.load(open(summary_config))
     else:
         config = None
-    summary_columns = "CHROM,POS,TUMOR_SAMPLE,NORMAL_SAMPLE,ID,UPS_Coord,ANN[*].GENE,ANN[*].EFFECT,ANN[*].HGVS_P," \
+    summary_columns = "CHROM,POS,TUMOR_SAMPLE,NORMAL_SAMPLE,ID,UPS_Coord,variantCaller,ANN[*].GENE,ANN[*].EFFECT,ANN[*].HGVS_P," \
         "SYMBOL,Variant_Classification,HGVSp_Short," \
         "TUMOR_MAF,NORMAL_MAF,TUMOR_DP,NORMAL_DP," \
         "ExAC_AF,MutationTaster_pred,provean_pred,FATHMM_pred,parssnp_pred," \

vcf_tools/somatic_vcf2tsv.py

@@ -126,7 +126,7 @@ def add_cancer_gene(df):
 
     chasm_pred_columns = [c for c in mdf.columns if "chasm_pred" in c]
     summary_columns = ("CHROM,POS,REF,ALT,SAMPLE.TUMOR,SAMPLE.NORMAL,"
-                       "UPS_Coord,SYMBOL,Variant_Classification,HGVSp_Short,"
+                       "variantCaller,UPS_Coord,SYMBOL,Variant_Classification,HGVSp_Short,"
                        "TUMOR_MAF,NORMAL_MAF,TUMOR_DP,NORMAL_DP,offTarget,"
                        "fuentes,dgd,oncoKB_level,oncoKB_cancer_type,"
                        "cancer_gene_census,kandoth,lawrence,num_cancer_gene,hap_insuf,"