Crg2 hg38

config_hpf.yaml → GRCh37/config_hpf.yaml

@@ -7,7 +7,7 @@ run:
   hpo: "" # five-column TSV with HPO terms; leave this string empty is there are no hpo terms
   flank: 100000
   gatk: "gatk"
-  pipeline: "wes" #either wes (exomes) or wgs (genomes) or annot (to annotate and produce reports for an input vcf) or mity (to generate mitochondrial reports)
+  pipeline: "wes" #either wes (exomes) or wgs (genomes) or annot (to annotate and produce reports for an input vcf)
   minio: ""
   PT_credentials: ""
 
@@ -82,11 +82,11 @@ qc:
 
 annotation:
   cre.vcfanno:
-    conf: "~/crg2/vcfanno/cre.vcfanno.conf"
+    conf: "~/crg2/vcfanno/cre.vcfanno_GRCh37.conf"
     lua_script: "~/crg2/vcfanno/cre.vcfanno.lua"
-    base_path: "/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/variation/"
+    base_path: "/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37"
   vcfanno:
-    conf: "~/crg2/vcfanno/crg.vcfanno.conf" 
+    conf: "~/crg2/vcfanno/crg.vcfanno_GRCh37.conf" 
     lua_script: "~/crg2/vcfanno/crg.vcfanno.lua"
     base_path: "/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/variation/"
   mt.vcfanno:
@@ -102,6 +102,7 @@ annotation:
     intron_bed: "/hpf/largeprojects/ccm_dccforge/dccdipg/Common/annotation/SVScore/refGene.introns.bed.gz"
     cadd: "/hpf/largeprojects/ccm_dccforge/dccdipg/Common/annotation/SVScore/whole_genome_SNVs.tsv.gz"
   svreport:
+    reference: GRCh37
     hgmd: "/hpf/largeprojects/ccm_dccforge/dccdipg/Common/annotation/HGMD_2018/hgmd_pro.db"
     protein_coding_genes: "/hpf/largeprojects/ccm_dccforge/dccdipg/Common/annotation/grch37.p13.ensembl.sorted.protein.coding.genes.bed"
     exon_bed: "/hpf/largeprojects/ccm_dccforge/dccdipg/Common/annotation/exons/hg19_UCSC_exons_canonical.bed"
@@ -121,7 +122,7 @@ annotation:
      database_path: "/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/variation/"
 
 validation:
-  benchmark: "benchmark_hpf.tsv"
+  benchmark: "benchmark.tsv"
 
 params:
   bwa:
@@ -135,9 +136,6 @@ params:
     #BaseRecalibrator: "--interval-set-rule INTERSECTION -U LENIENT-VCF-PROCESSING --read-filter BadCigar --read-filter NotzPrimaryAlignment"
     GenotypeGVCFs: ""
     VariantRecalibrator: ""
-    Mutect2: 
-      gnomad_germline: "/hpf/largeprojects/ccm_dccforge/dccdipg/Common/annotation/Mutect2/af-only-gnomad.raw.sites.vcf"
-    FilterMutectCalls: ""
   gatk3:
     java_opts: "-Xms500m -Xmx9555m"
     HaplotypeCaller: "-drf DuplicateRead --interval_set_rule INTERSECTION --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment"
@@ -173,14 +171,10 @@ params:
   bcftools:
     mpileup: "-a DP -a AD "
     call: " -m -v "
-    # -F x sets the output filter to PASS if any of the variant filters is PASS in sample VCFs to be merged
-    merge: "-F x"
-  freebayes:
-    call: " --genotype-qualities --strict-vcf --ploidy 2 --no-partial-observations --min-repeat-entropy 1 "
+  freebayes: " --genotype-qualities --strict-vcf --ploidy 2 --no-partial-observations --min-repeat-entropy 1 "
   platypus: "--filterDuplicates=0"
   rtg-tools:
     java_opts: "-Xmx20g"
     vcfeval:
       sdf: "/hpf/largeprojects/ccm_dccforge/dccdipg/Common/rtg-tools/GRch37_SDF/"
-    vcfsubset:
-      java_opts: "-Xmx2048m"
+