fix: change indel reference

CCBR · Mar 7, 2024 · 18a471a · 18a471a
1 parent 4c53015
commit 18a471a
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/conf/genomes.config b/conf/genomes.config
@@ -9,10 +9,10 @@ params {
             intervals= "${projectDir}/assets/hg38_v0_wgs_calling_regions.hg38.bed"
             //millsindel = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz" //Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
             //shapeitindel =  "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz" //ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz" //file(params.gold_indels2) //
-            KNOWNINDELS= '/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/dbsnp_indel.vcf'
+            KNOWNINDELS= '/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz'
             KNOWNRECAL = '--known-sites /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/GATK_resource_bundle/dbsnp_138.hg38.vcf.gz --known-sites /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/GATK_resource_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --known-sites /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/GATK_resource_bundle/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz'
             dbsnp = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/dbsnp_138.hg38.vcf.gz"
-            dbsnp_indel = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/dbsnp_indel.vcf"
+            dbsnp_indel = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
             gnomad = '--germline-resource /data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GNOMAD/somatic-hg38-af-only-gnomad.hg38.vcf.gz' // /data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GNOMAD/somatic-hg38-af-only-gnomad.hg38.vcf.gz
             pon = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/PON/updatedpon.vcf.gz"    //pon="/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/PON/hg38.noCOSMIC_ClinVar.pon.vcf.gz" //file{params.pon}
             kgp = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz"