feat: vep 113 and AlphaMissense

genomic-medicine-sweden · Oct 21, 2024 · 797f59f · 797f59f
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commit 797f59f
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Showing 17 changed files with 16 additions and 281 deletions.
diff --git a/config/config.data.hg19.yaml b/config/config.data.hg19.yaml
@@ -171,10 +171,10 @@ tmb_umi:
   filter_genes: "{{PROJECT_DESIGN_DATA}}/GMS560/tmb/tmb_filter_genes.txt"
 
 vep:
-  vep_cache:  "{{PROJECT_REF_DATA}}/ref_data/vep/105"
-  extra: " --assembly GRCh37 --check_existing --pick --sift b --polyphen b --ccds --uniprot --hgvs --symbol --numbers --domains --regulatory --canonical --protein --biotype --uniprot --tsl --appris --gene_phenotype --af --af_1kg --af_gnomad --max_af --pubmed --variant_class "
+  vep_cache:  "{{PROJECT_REF_DATA}}/ref_data/vep/113"
+  extra: " --assembly GRCh37 --plugin AlphaMissense,file={{PROJECT_REF_DATA}}/ref_data/vep/plugin/AlphaMissense_hg19.tsv.gz --check_existing --pick --sift b --polyphen b --ccds --hgvs --symbol --numbers --domains --regulatory --canonical --protein --biotype --uniprot --tsl --appris --gene_phenotype --af --af_1kg --af_gnomad --max_af --pubmed --variant_class "
 
 vep_wo_pick:
-  vep_cache:  "{{PROJECT_REF_DATA}}/ref_data/vep/105"
-  extra: " --assembly GRCh37 --check_existing --sift b --polyphen b --ccds --uniprot --hgvs --symbol --numbers --domains --regulatory --canonical --protein --biotype --uniprot --tsl --appris --gene_phenotype --af --af_1kg --af_gnomad --max_af --pubmed --variant_class "
+  vep_cache:  "{{PROJECT_REF_DATA}}/ref_data/vep/113"
+  extra: " --assembly GRCh37 --plugin AlphaMissense,file={{PROJECT_REF_DATA}}/ref_data/vep/plugin/AlphaMissense_hg19.tsv.gz --check_existing --sift b --polyphen b --ccds --hgvs --symbol --numbers --domains --regulatory --canonical --protein --biotype --uniprot --tsl --appris --gene_phenotype --af --af_1kg --af_gnomad --max_af --pubmed --variant_class "
 
diff --git a/config/config.data.hg38.yaml b/config/config.data.hg38.yaml
@@ -168,9 +168,9 @@ tmb_umi:
   filter_genes: "{{PROJECT_DESIGN_DATA}}/GMS560/tmb/tmb_filter_genes.txt"
 
 vep:
-  vep_cache:  "{{PROJECT_REF_DATA}}/ref_data/vep/105"
-  extra: " --assembly GRCh38 --check_existing --pick --sift b --polyphen b --ccds --uniprot --hgvs --symbol --numbers --domains --regulatory --canonical --protein --biotype --uniprot --tsl --appris --gene_phenotype --af --af_1kg --af_gnomad --max_af --pubmed --variant_class "
+  vep_cache:  "{{PROJECT_REF_DATA}}/ref_data/vep/113"
+  extra: " --assembly GRCh38 --plugin AlphaMissense,file={{PROJECT_REF_DATA}}/ref_data/vep/plugin/AlphaMissense_hg38.tsv.gz --check_existing --pick --sift b --polyphen b --ccds --hgvs --symbol --numbers --domains --regulatory --canonical --protein --biotype --uniprot --tsl --appris --gene_phenotype --af --af_1kg --af_gnomad --max_af --pubmed --variant_class "
 
 vep_wo_pick:
-  vep_cache:  "{{PROJECT_REF_DATA}}/ref_data/vep/105"
-  extra: " --assembly GRCh38 --check_existing --sift b --polyphen b --ccds --uniprot --hgvs --symbol --numbers --domains --regulatory --canonical --protein --biotype --uniprot --tsl --appris --gene_phenotype --af --af_1kg --af_gnomad --max_af --pubmed --variant_class "
+  vep_cache:  "{{PROJECT_REF_DATA}}/ref_data/vep/113"
+  extra: " --assembly GRCh38 --plugin AlphaMissense,file={{PROJECT_REF_DATA}}/ref_data/vep/plugin/AlphaMissense_hg38.tsv.gz --check_existing --sift b --polyphen b --ccds --hgvs --symbol --numbers --domains --regulatory --canonical --protein --biotype --uniprot --tsl --appris --gene_phenotype --af --af_1kg --af_gnomad --max_af --pubmed --variant_class "
diff --git a/config/config.yaml b/config/config.yaml
@@ -129,14 +129,14 @@ fgbio_group_reads_by_umi:
   umi_strategy: paired
 
 filter_vcf:
-  snv_soft_filter: "config/filters/config_soft_filter_uppsala_vep105.yaml"
-  snv_soft_filter_umi: "config/filters/config_soft_filter_umi_vep105.yaml"
-  snv_hard_filter: "config/filters/config_hard_filter_uppsala_vep105.yaml"
-  snv_hard_filter_umi: "config/filters/config_hard_filter_umi_vep105.yaml"
+  snv_soft_filter: "config/filters/config_soft_filter.yaml"
+  snv_soft_filter_umi: "config/filters/config_soft_filter_umi.yaml"
+  snv_hard_filter: "config/filters/config_hard_filter.yaml"
+  snv_hard_filter_umi: "config/filters/config_hard_filter_umi.yaml"
   snv_hard_filter_purecn: "config/filters/config_hard_filter_purecn.yaml"
   cnv_hard_filter_amp: "config/filters/config_hard_filter_cnv_amp.yaml"
   cnv_hard_filter_loh: "config/filters/config_hard_filter_cnv_loh.yaml"
-  germline: "config/filters/config_hard_filter_germline_vep105.yaml"
+  germline: "config/filters/config_hard_filter_germline.yaml"
 
 filter_fuseq_wes:
   min_support: 50
@@ -406,7 +406,7 @@ vardict:
   extra: "-Q 1"
 
 vep:
-  container: "docker://hydragenetics/vep:105"
+  container: "docker://hydragenetics/vep:113"
   mode: --offline --cache --refseq
 
 vep_wo_pick:

diff --git a/...rs/config_hard_filter_uppsala_vep107.yaml → config/filters/config_hard_filter.yaml b/...rs/config_hard_filter_uppsala_vep107.yaml → config/filters/config_hard_filter.yaml
diff --git a/...s/config_hard_filter_germline_vep107.yaml → .../filters/config_hard_filter_germline.yaml b/...s/config_hard_filter_germline_vep107.yaml → .../filters/config_hard_filter_germline.yaml
diff --git a/config/filters/config_hard_filter_germline_vep105.yaml b/config/filters/config_hard_filter_germline_vep105.yaml
diff --git a/...ilters/config_hard_filter_umi_vep105.yaml → config/filters/config_hard_filter_umi.yaml b/...ilters/config_hard_filter_umi_vep105.yaml → config/filters/config_hard_filter_umi.yaml
@@ -13,7 +13,7 @@ filters:
     soft_filter: "False"
   germline:
     description: "Hard filter germline"
-    expression: "(VEP:gnomAD_AF > 0.005)"
+    expression: "(VEP:gnomADe_AF > 0.005)"
     soft_filter: "False"
   af_snv:
     description: "Hard filter SNV variants with low vaf"

diff --git a/config/filters/config_hard_filter_uppsala_vep105.yaml b/config/filters/config_hard_filter_uppsala_vep105.yaml
diff --git a/config/filters/config_hard_filter_vep105.yaml b/config/filters/config_hard_filter_vep105.yaml
diff --git a/config/filters/config_hard_filter_vep107.yaml b/config/filters/config_hard_filter_vep107.yaml
diff --git a/...rs/config_soft_filter_uppsala_vep107.yaml → config/filters/config_soft_filter.yaml b/...rs/config_soft_filter_uppsala_vep107.yaml → config/filters/config_soft_filter.yaml
diff --git a/...ilters/config_soft_filter_umi_vep105.yaml → config/filters/config_soft_filter_umi.yaml b/...ilters/config_soft_filter_umi_vep105.yaml → config/filters/config_soft_filter_umi.yaml
@@ -16,7 +16,7 @@ filters:
     soft_filter: "True"
   germline:
     description: "Hard filter germline"
-    expression: "(VEP:gnomAD_AF > 0.005)"
+    expression: "(VEP:gnomADe_AF > 0.005)"
     soft_filter_flag: "germline_gnomad"
     soft_filter: "True"
   af_snv:

diff --git a/config/filters/config_soft_filter_uppsala_vep105.yaml b/config/filters/config_soft_filter_uppsala_vep105.yaml
diff --git a/config/filters/config_soft_filter_vep105.yaml b/config/filters/config_soft_filter_vep105.yaml
diff --git a/config/filters/config_soft_filter_vep107.yaml b/config/filters/config_soft_filter_vep107.yaml
diff --git a/config/references/config.vep105.yaml b/config/references/config.vep105.yaml
diff --git a/config/references/config.vep107.yaml b/config/references/config.vep107.yaml