From 797f59fb6e5cd1af095509a4bacae210a57cffaf Mon Sep 17 00:00:00 2001 From: jonca79 Date: Mon, 21 Oct 2024 10:58:21 +0200 Subject: [PATCH] feat: vep 113 and AlphaMissense --- config/config.data.hg19.yaml | 8 ++-- config/config.data.hg38.yaml | 8 ++-- config/config.yaml | 12 +++--- ...la_vep107.yaml => config_hard_filter.yaml} | 0 ....yaml => config_hard_filter_germline.yaml} | 0 .../config_hard_filter_germline_vep105.yaml | 13 ------ ...ep105.yaml => config_hard_filter_umi.yaml} | 2 +- .../config_hard_filter_uppsala_vep105.yaml | 33 --------------- config/filters/config_hard_filter_vep105.yaml | 33 --------------- config/filters/config_hard_filter_vep107.yaml | 33 --------------- ...la_vep107.yaml => config_soft_filter.yaml} | 0 ...ep105.yaml => config_soft_filter_umi.yaml} | 2 +- .../config_soft_filter_uppsala_vep105.yaml | 41 ------------------- config/filters/config_soft_filter_vep105.yaml | 41 ------------------- config/filters/config_soft_filter_vep107.yaml | 41 ------------------- config/references/config.vep105.yaml | 13 ------ config/references/config.vep107.yaml | 17 -------- 17 files changed, 16 insertions(+), 281 deletions(-) rename config/filters/{config_hard_filter_uppsala_vep107.yaml => config_hard_filter.yaml} (100%) rename config/filters/{config_hard_filter_germline_vep107.yaml => config_hard_filter_germline.yaml} (100%) delete mode 100644 config/filters/config_hard_filter_germline_vep105.yaml rename config/filters/{config_hard_filter_umi_vep105.yaml => config_hard_filter_umi.yaml} (98%) delete mode 100644 config/filters/config_hard_filter_uppsala_vep105.yaml delete mode 100644 config/filters/config_hard_filter_vep105.yaml delete mode 100644 config/filters/config_hard_filter_vep107.yaml rename config/filters/{config_soft_filter_uppsala_vep107.yaml => config_soft_filter.yaml} (100%) rename config/filters/{config_soft_filter_umi_vep105.yaml => config_soft_filter_umi.yaml} (98%) delete mode 100644 config/filters/config_soft_filter_uppsala_vep105.yaml delete mode 100644 config/filters/config_soft_filter_vep105.yaml delete mode 100644 config/filters/config_soft_filter_vep107.yaml delete mode 100644 config/references/config.vep105.yaml delete mode 100644 config/references/config.vep107.yaml diff --git a/config/config.data.hg19.yaml b/config/config.data.hg19.yaml index b5f2dabf..77c9f219 100644 --- 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 index bf9c3ef4..7111f64f 100644 --- 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 index b1dd8e99..04dfa7ff 100644 --- 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/config/filters/config_hard_filter_uppsala_vep107.yaml b/config/filters/config_hard_filter.yaml similarity index 100% rename from config/filters/config_hard_filter_uppsala_vep107.yaml rename to config/filters/config_hard_filter.yaml diff --git a/config/filters/config_hard_filter_germline_vep107.yaml b/config/filters/config_hard_filter_germline.yaml similarity index 100% rename from config/filters/config_hard_filter_germline_vep107.yaml rename to config/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 deleted file mode 100644 index 0d0f2702..00000000 --- a/config/filters/config_hard_filter_germline_vep105.yaml +++ /dev/null @@ -1,13 +0,0 @@ -filters: - germline: - description: "Hard filter germline" - expression: "(VEP:gnomAD_AF < 0.001)" - soft_filter: "False" - ad: - description: "Hard filter variants with few observations (AD lower than 20)" - expression: "(FORMAT:AD:1 < 20 or FORMAT:AD:0 < 20)" - soft_filter: "False" - snp_type: - description: "Hard filter variants that are not SNVs" - expression: "(!exist[SNV, VEP:VARIANT_CLASS])" - soft_filter: "False" diff --git a/config/filters/config_hard_filter_umi_vep105.yaml b/config/filters/config_hard_filter_umi.yaml similarity index 98% rename from config/filters/config_hard_filter_umi_vep105.yaml rename to config/filters/config_hard_filter_umi.yaml index a66e2b12..7454a5f0 100644 --- a/config/filters/config_hard_filter_umi_vep105.yaml +++ b/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 deleted file mode 100644 index 03f0e1b1..00000000 --- a/config/filters/config_hard_filter_uppsala_vep105.yaml +++ /dev/null @@ -1,33 +0,0 @@ -filters: - intron: - description: "Hard filter intronic variants" - expression: "(exist[intron_variant, VEP:Consequence] and !exist[splice, VEP:Consequence] and VEP:SYMBOL != MET and VEP:SYMBOL != TERT and !exist[COSV[0-9]+, VEP:Existing_variation])" - soft_filter: "False" - vaf: - description: "Hard filter variants with low vaf (AF lower than 0.01)" - expression: "(FORMAT:AF:0 < 0.01)" - soft_filter: "False" - artifacts: - description: "Hard filter variants found in more than 3 normal samples" - expression: "((INFO:Artifact:0 > 3 and INFO:ArtifactNrSD:0 < 5) or (INFO:Artifact:1 > 3 and INFO:ArtifactNrSD:1 < 5))" - soft_filter: "False" - background: - description: "Hard filter position with where backgound distribution overlaps variant (lower than 4 SD from median)" - expression: "(INFO:PositionNrSD < 4 and !exist[1-hotspot, INFO:Hotspot])" - soft_filter: "False" - germline: - description: "Hard filter germline" - expression: "(VEP:gnomAD_AF > 0.005)" - soft_filter: "False" - ad: - description: "Hard filter variants with few observations (AD lower than 20)" - expression: "(FORMAT:AD:1 < 20 and !exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL != TERT)" - soft_filter: "False" - ad_hotspot: - description: "Hard filter hotspot variants with few observations (AD lower than 10)" - expression: "(FORMAT:AD:1 < 10 and exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL != TERT)" - soft_filter: "False" - ad_TERT: - description: "Hard filter TERT variants with few observations (AD lower than 4)" - expression: "(FORMAT:AD:1 < 4 and exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL = TERT)" - soft_filter: "False" diff --git a/config/filters/config_hard_filter_vep105.yaml b/config/filters/config_hard_filter_vep105.yaml deleted file mode 100644 index 369e45e1..00000000 --- a/config/filters/config_hard_filter_vep105.yaml +++ /dev/null @@ -1,33 +0,0 @@ -filters: - intron: - description: "Hard filter intronic variants" - expression: "(exist[intron_variant, VEP:Consequence] and !exist[splice, VEP:Consequence] and VEP:SYMBOL != MET and VEP:SYMBOL != TERT and !exist[COSV[0-9]+, VEP:Existing_variation])" - soft_filter: "False" - vaf: - description: "Hard filter variants with low vaf (AF lower than 0.01)" - expression: "(FORMAT:AF:0 < 0.01)" - soft_filter: "False" - artifacts: - description: "Hard filter variants found in more than 3 normal samples" - expression: "(INFO:Artifact:0 > 3 or INFO:Artifact:1 > 3)" - soft_filter: "False" - background: - description: "Hard filter position with where backgound distribution overlaps variant (lower than 4 SD from median)" - expression: "(INFO:PositionNrSD < 4 and !exist[1-hotspot, INFO:Hotspot])" - soft_filter: "False" - germline: - description: "Hard filter germline" - expression: "(VEP:gnomAD_AF > 0.005)" - soft_filter: "False" - ad: - description: "Hard filter variants with few observations (AD lower than 20)" - expression: "(FORMAT:AD:1 < 20 and !exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL != TERT)" - soft_filter: "False" - ad_hotspot: - description: "Hard filter hotspot variants with few observations (AD lower than 10)" - expression: "(FORMAT:AD:1 < 10 and exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL != TERT)" - soft_filter: "False" - ad_TERT: - description: "Hard filter TERT variants with few observations (AD lower than 4)" - expression: "(FORMAT:AD:1 < 4 and exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL = TERT)" - soft_filter: "False" diff --git a/config/filters/config_hard_filter_vep107.yaml b/config/filters/config_hard_filter_vep107.yaml deleted file mode 100644 index 7b46c4f4..00000000 --- a/config/filters/config_hard_filter_vep107.yaml +++ /dev/null @@ -1,33 +0,0 @@ -filters: - intron: - description: "Hard filter intronic variants" - expression: "(exist[intron_variant, VEP:Consequence] and !exist[splice, VEP:Consequence] and VEP:SYMBOL != MET and VEP:SYMBOL != TERT and !exist[COSV[0-9]+, VEP:Existing_variation])" - soft_filter: "False" - vaf: - description: "Hard filter variants with low vaf (AF lower than 0.01)" - expression: "(FORMAT:AF:0 < 0.01)" - soft_filter: "False" - artifacts: - description: "Hard filter variants found in more than 3 normal samples" - expression: "(INFO:Artifact:0 > 3 or INFO:Artifact:1 > 3)" - soft_filter: "False" - background: - description: "Hard filter position with where backgound distribution overlaps variant (lower than 4 SD from median)" - expression: "(INFO:PositionNrSD < 4 and !exist[1-hotspot, INFO:Hotspot])" - soft_filter: "False" - germline: - description: "Hard filter germline exon" - expression: "(VEP:gnomADe_AF > 0.005)" - soft_filter: "False" - ad: - description: "Hard filter variants with few observations (AD lower than 20)" - expression: "(FORMAT:AD:1 < 20 and !exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL != TERT)" - soft_filter: "False" - ad_hotspot: - description: "Hard filter hotspot variants with few observations (AD lower than 10)" - expression: "(FORMAT:AD:1 < 10 and exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL != TERT)" - soft_filter: "False" - ad_TERT: - description: "Hard filter TERT variants with few observations (AD lower than 4)" - expression: "(FORMAT:AD:1 < 4 and exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL = TERT)" - soft_filter: "False" diff --git a/config/filters/config_soft_filter_uppsala_vep107.yaml b/config/filters/config_soft_filter.yaml similarity index 100% rename from config/filters/config_soft_filter_uppsala_vep107.yaml rename to config/filters/config_soft_filter.yaml diff --git a/config/filters/config_soft_filter_umi_vep105.yaml b/config/filters/config_soft_filter_umi.yaml similarity index 98% rename from config/filters/config_soft_filter_umi_vep105.yaml rename to config/filters/config_soft_filter_umi.yaml index dda54549..68708771 100644 --- a/config/filters/config_soft_filter_umi_vep105.yaml +++ b/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 deleted file mode 100644 index d5349d92..00000000 --- a/config/filters/config_soft_filter_uppsala_vep105.yaml +++ /dev/null @@ -1,41 +0,0 @@ -filters: - intron: - description: "Soft filter intronic variants" - expression: "(exist[intron_variant, VEP:Consequence] and !exist[splice, VEP:Consequence] and VEP:SYMBOL != MET and VEP:SYMBOL != TERT and !exist[COSV[0-9]+, VEP:Existing_variation])" - soft_filter_flag: "Intronic" - soft_filter: "True" - vaf: - description: "Soft filter variants with low vaf (AF lower than 0.01)" - expression: "(FORMAT:AF:0 < 0.01)" - soft_filter_flag: "AF_lt_0.01" - soft_filter: "True" - artifacts: - description: "Soft filter variants found in more than 3 normal samples" - expression: "((INFO:Artifact:0 > 3 and INFO:ArtifactNrSD:0 < 5) or (INFO:Artifact:1 > 3 and INFO:ArtifactNrSD:1 < 5))" - soft_filter_flag: "Artifact_gt_3" - soft_filter: "True" - background: - description: "Soft filter position with where backgound distribution overlaps variant (lower than 4 SD from median)" - expression: "(INFO:PositionNrSD < 4 and !exist[1-hotspot, INFO:Hotspot])" - soft_filter_flag: "Background_lt_4" - soft_filter: "True" - germline: - description: "Soft filter germline SNVs based on GnomAD" - expression: "(VEP:gnomAD_AF > 0.005)" - soft_filter_flag: "Germline" - soft_filter: "True" - ad: - description: "Soft filter variants with few observations (AD lower than 20)" - expression: "(FORMAT:AD:1 < 20 and !exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL != TERT)" - soft_filter_flag: "AD_lt_20" - soft_filter: "True" - ad_hotspot: - description: "Soft filter hotspot variants with few observations (AD lower than 10)" - expression: "(FORMAT:AD:1 < 10 and exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL != TERT)" - soft_filter_flag: "AD_HS_lt_10" - soft_filter: "True" - ad_TERT: - description: "Soft filter TERT variants with few observations (AD lower than 4)" - expression: "(FORMAT:AD:1 < 4 and exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL = TERT)" - soft_filter_flag: "AD_TERT_lt_4" - soft_filter: "True" diff --git a/config/filters/config_soft_filter_vep105.yaml b/config/filters/config_soft_filter_vep105.yaml deleted file mode 100644 index 6ab492fe..00000000 --- a/config/filters/config_soft_filter_vep105.yaml +++ /dev/null @@ -1,41 +0,0 @@ -filters: - intron: - description: "Soft filter intronic variants" - expression: "(exist[intron_variant, VEP:Consequence] and !exist[splice, VEP:Consequence] and VEP:SYMBOL != MET and VEP:SYMBOL != TERT and !exist[COSV[0-9]+, VEP:Existing_variation])" - soft_filter_flag: "Intronic" - soft_filter: "True" - vaf: - description: "Soft filter variants with low vaf (AF lower than 0.01)" - expression: "(FORMAT:AF:0 < 0.01)" - soft_filter_flag: "AF_lt_0.01" - soft_filter: "True" - artifacts: - description: "Soft filter variants found in more than 3 normal samples" - expression: "(INFO:Artifact:0 > 3 or INFO:Artifact:1 > 3)" - soft_filter_flag: "Artifact_gt_3" - soft_filter: "True" - background: - description: "Soft filter position with where backgound distribution overlaps variant (lower than 4 SD from median)" - expression: "(INFO:PositionNrSD < 4 and !exist[1-hotspot, INFO:Hotspot])" - soft_filter_flag: "Background_lt_4" - soft_filter: "True" - germline: - description: "Soft filter germline SNVs based on GnomAD" - expression: "(VEP:gnomAD_AF > 0.005)" - soft_filter_flag: "Germline" - soft_filter: "True" - ad: - description: "Soft filter variants with few observations (AD lower than 20)" - expression: "(FORMAT:AD:1 < 20 and !exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL != TERT)" - soft_filter_flag: "AD_lt_20" - soft_filter: "True" - ad_hotspot: - description: "Soft filter hotspot variants with few observations (AD lower than 10)" - expression: "(FORMAT:AD:1 < 10 and exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL != TERT)" - soft_filter_flag: "AD_HS_lt_10" - soft_filter: "True" - ad_TERT: - description: "Soft filter TERT variants with few observations (AD lower than 4)" - expression: "(FORMAT:AD:1 < 4 and exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL = TERT)" - soft_filter_flag: "AD_TERT_lt_4" - soft_filter: "True" diff --git a/config/filters/config_soft_filter_vep107.yaml b/config/filters/config_soft_filter_vep107.yaml deleted file mode 100644 index f0a0c575..00000000 --- a/config/filters/config_soft_filter_vep107.yaml +++ /dev/null @@ -1,41 +0,0 @@ -filters: - intron: - description: "Soft filter intronic variants" - expression: "(exist[intron_variant, VEP:Consequence] and !exist[splice, VEP:Consequence] and VEP:SYMBOL != MET and VEP:SYMBOL != TERT and !exist[COSV[0-9]+, VEP:Existing_variation])" - soft_filter_flag: "Intronic" - soft_filter: "True" - vaf: - description: "Soft filter variants with low vaf (AF lower than 0.01)" - expression: "(FORMAT:AF:0 < 0.01)" - soft_filter_flag: "AF_lt_0.01" - soft_filter: "True" - artifacts: - description: "Soft filter variants found in more than 3 normal samples" - expression: "(INFO:Artifact:0 > 3 or INFO:Artifact:1 > 3)" - soft_filter_flag: "Artifact_gt_3" - soft_filter: "True" - background: - description: "Soft filter position with where backgound distribution overlaps variant (lower than 4 SD from median)" - expression: "(INFO:PositionNrSD < 4 and !exist[1-hotspot, INFO:Hotspot])" - soft_filter_flag: "Background_lt_4" - soft_filter: "True" - germline: - description: "Soft filter germline SNVs based on GnomAD exon" - expression: "(VEP:gnomADe_AF > 0.005)" - soft_filter_flag: "Germline" - soft_filter: "True" - ad: - description: "Soft filter variants with few observations (AD lower than 20)" - expression: "(FORMAT:AD:1 < 20 and !exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL != TERT)" - soft_filter_flag: "AD_lt_20" - soft_filter: "True" - ad_hotspot: - description: "Soft filter hotspot variants with few observations (AD lower than 10)" - expression: "(FORMAT:AD:1 < 10 and exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL != TERT)" - soft_filter_flag: "AD_HS_lt_10" - soft_filter: "True" - ad_TERT: - description: "Soft filter TERT variants with few observations (AD lower than 4)" - expression: "(FORMAT:AD:1 < 4 and exist[1-hotspot, INFO:Hotspot] and VEP:SYMBOL = TERT)" - soft_filter_flag: "AD_TERT_lt_4" - soft_filter: "True" diff --git a/config/references/config.vep105.yaml b/config/references/config.vep105.yaml deleted file mode 100644 index 78bfa6b6..00000000 --- a/config/references/config.vep105.yaml +++ /dev/null @@ -1,13 +0,0 @@ ---- - - filter_vcf: - snv_soft_filter: - path: "config/filters/config_soft_filter_uppsala_vep105.yaml" - snv_hard_filter: - path: "config/filters/config_hard_filter_uppsala_vep105.yaml" - cnv_hard_filter_amp: - path: "config/filters/config_hard_filter_cnv_amp.yaml" - cnv_hard_filter_loh: - path: "config/filters/config_hard_filter_cnv_loh.yaml" - germline: - path: "config/filters/config_hard_filter_germline_vep105.yaml" \ No newline at end of file diff --git a/config/references/config.vep107.yaml b/config/references/config.vep107.yaml deleted file mode 100644 index c119f0de..00000000 --- a/config/references/config.vep107.yaml +++ /dev/null @@ -1,17 +0,0 @@ ---- - - cnv_html_report: - template: - path: config/reports/cnv_report_template.html - - filter_vcf: - snv_soft_filter: - path: "config/filters/config_soft_filter_uppsala_vep107.yaml" - snv_hard_filter: - path: "config/filters/config_hard_filter_uppsala_vep107.yaml" - cnv_hard_filter_amp: - path: "config/filters/config_hard_filter_cnv_amp.yaml" - cnv_hard_filter_loh: - path: "config/filters/config_hard_filter_cnv_loh.yaml" - germline: - path: "config/filters/config_hard_filter_germline_vep107.yaml" \ No newline at end of file