Merge pull request #48 from eastgenomics/NG-298

Restore gnomad nhomalt in reports (#48) Co-Authored-By: Matt <[email protected]>
eastgenomics · Nov 23, 2023 · dbee186 · dbee186
2 parents 16558ac + 55a8fe2
commit dbee186
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/egg5_config_v2.3.2.py b/egg5_config_v2.3.2.py
@@ -72,15 +72,15 @@
     "{}.config_file ID".format(vep_stage_id): vep_config,
     "{}.config_file".format(vep_stage_id): "",
     # inputs for generate_variant_workbook
-    "{}.exclude_columns".format(generate_workbook_stage_id): "BaseQRankSum ClippingRankSum DB ExcessHet FS MLEAC MLEAF MQ MQRankSum QD ReadPosRankSum SOR PL QUAL ID FILTER  CSQ_ClinVar_CLNSIGCONF  CSQ_Allele CSQ_HGNC_ID DP AC AF AN CSQ_SpliceAI_pred_DP_AL CSQ_SpliceAI_pred_DP_AG CSQ_SpliceAI_pred_DP_DG CSQ_SpliceAI_pred_DP_DL CSQ_gnomADe_AC_popmax CSQ_gnomADe_AF_popmax CSQ_gnomADe_AN_popmax CSQ_gnomADe_nhomalt CSQ_gnomADe_nhomalt_popmax CSQ_gnomADe_non_cancer_AC CSQ_gnomADe_non_cancer_AC_popmax CSQ_gnomADe_non_cancer_AF CSQ_gnomADe_non_cancer_AF_popmax CSQ_gnomADe_non_cancer_AN CSQ_gnomADe_non_cancer_AN_popmax CSQ_gnomADe_non_cancer_nhomalt CSQ_gnomADe_non_cancer_nhomalt_popmax CSQ_gnomADe_non_cancer_popmax CSQ_gnomADe_popmax CSQ_gnomADg_AC_popmax CSQ_gnomADg_AF_popmax CSQ_gnomADg_AN_popmax CSQ_gnomADg_nhomalt CSQ_gnomADg_nhomalt_popmax CSQ_gnomADg_popmax",
+    "{}.exclude_columns".format(generate_workbook_stage_id): "BaseQRankSum ClippingRankSum DB ExcessHet FS MLEAC MLEAF MQ MQRankSum QD ReadPosRankSum SOR PL QUAL ID FILTER  CSQ_ClinVar_CLNSIGCONF  CSQ_Allele CSQ_HGNC_ID DP AC AF AN CSQ_SpliceAI_pred_DP_AL CSQ_SpliceAI_pred_DP_AG CSQ_SpliceAI_pred_DP_DG CSQ_SpliceAI_pred_DP_DL CSQ_gnomADe_AC_popmax CSQ_gnomADe_AF_popmax CSQ_gnomADe_AN_popmax CSQ_gnomADe_nhomalt_popmax CSQ_gnomADe_non_cancer_AC CSQ_gnomADe_non_cancer_AC_popmax CSQ_gnomADe_non_cancer_AF CSQ_gnomADe_non_cancer_AF_popmax CSQ_gnomADe_non_cancer_AN CSQ_gnomADe_non_cancer_AN_popmax CSQ_gnomADe_non_cancer_nhomalt CSQ_gnomADe_non_cancer_nhomalt_popmax CSQ_gnomADe_non_cancer_popmax CSQ_gnomADe_popmax CSQ_gnomADg_AC_popmax CSQ_gnomADg_AF_popmax CSQ_gnomADg_AN_popmax CSQ_gnomADg_nhomalt_popmax CSQ_gnomADg_popmax",
     "{}.acmg".format(generate_workbook_stage_id): "true",
     "{}.rename_columns".format(generate_workbook_stage_id): "CSQ_Feature=Transcript DP_FMT=DP",
     "{}.add_comment_column".format(generate_workbook_stage_id): "true",
     "{}.keep_tmp".format(generate_workbook_stage_id): "true",
     "{}.summary".format(generate_workbook_stage_id): "dias",
     "{}.filter".format(generate_workbook_stage_id): "bcftools filter -e '(CSQ_Consequence==\"synonymous_variant\" | CSQ_Consequence==\"intron_variant\" | CSQ_Consequence==\"upstream_gene_variant\" | CSQ_Consequence==\"downstream_gene_variant\" | CSQ_Consequence==\"intergenic_variant\" | CSQ_Consequence==\"5_prime_UTR_variant\" | CSQ_Consequence==\"3_prime_UTR_variant\" | CSQ_gnomADe_AF>0.01 | CSQ_gnomADg_AF>0.01 | CSQ_TWE_AF>0.05) & CSQ_HGMD_CLASS!~ \"DM\" & CSQ_ClinVar_CLNSIG!~ \"pathogenic\\/i\" & CSQ_ClinVar_CLNSIGCONF!~ \"pathogenic\\/i\"'",
     "{}.human_filter".format(generate_workbook_stage_id): "excluded gnomAD exomes / genomes > 1%, TWE > 5%, synonymous / intronic / intergenic / upstream / downstream / UTRs EXCEPT pathogenic status in ClinVar OR DM in HGMD Class",
-    "{}.reorder_columns".format(generate_workbook_stage_id): "CHROM POS REF ALT GT GQ DP_FMT AD CSQ_SYMBOL CSQ_EXON CSQ_INTRON CSQ_HGVSc CSQ_HGVSp CSQ_Consequence CSQ_IMPACT CSQ_VARIANT_CLASS CSQ_gnomADe_AF CSQ_gnomADe_Hom CSQ_gnomADe_AC CSQ_gnomADe_AN CSQ_gnomADg_AF CSQ_gnomADg_AC CSQ_gnomADg_AN CSQ_TWE_AF CSQ_TWE_AC_Hom CSQ_TWE_AC_Het CSQ_TWE_AN CSQ_HGMD CSQ_HGMD_CLASS CSQ_HGMD_RANKSCORE CSQ_HGMD_PHEN CSQ_Existing_variation CSQ_ClinVar CSQ_ClinVar_CLNDN CSQ_ClinVar_CLNSIG CSQ_Mastermind_MMID3 CSQ_CADD_PHRED CSQ_REVEL CSQ_SpliceAI_pred_DS_AG CSQ_SpliceAI_pred_DS_AL CSQ_SpliceAI_pred_DS_DG CSQ_SpliceAI_pred_DS_DL CSQ_HGVS_OFFSET CSQ_STRAND CSQ_Feature",
+    "{}.reorder_columns".format(generate_workbook_stage_id): "CHROM POS REF ALT GT GQ DP_FMT AD CSQ_SYMBOL CSQ_EXON CSQ_INTRON CSQ_HGVSc CSQ_HGVSp CSQ_Consequence CSQ_IMPACT CSQ_VARIANT_CLASS CSQ_gnomADe_AF CSQ_gnomADe_Hom CSQ_gnomADe_AC CSQ_gnomADe_AN CSQ_gnomADe_nhomalt CSQ_gnomADg_AF CSQ_gnomADg_AC CSQ_gnomADg_AN CSQ_gnomADg_nhomalt CSQ_TWE_AF CSQ_TWE_AC_Hom CSQ_TWE_AC_Het CSQ_TWE_AN CSQ_HGMD CSQ_HGMD_CLASS CSQ_HGMD_RANKSCORE CSQ_HGMD_PHEN CSQ_Existing_variation CSQ_ClinVar CSQ_ClinVar_CLNDN CSQ_ClinVar_CLNSIG CSQ_Mastermind_MMID3 CSQ_CADD_PHRED CSQ_REVEL CSQ_SpliceAI_pred_DS_AG CSQ_SpliceAI_pred_DS_AL CSQ_SpliceAI_pred_DS_DG CSQ_SpliceAI_pred_DS_DL CSQ_HGVS_OFFSET CSQ_STRAND CSQ_Feature",
     "{}.freeze_column".format(generate_workbook_stage_id): "",
     # inputs for generate bed for athena
     "{}.exons_nirvana ID".format(generate_bed_athena_stage_id): exons_nirvana,