From 55a8fe275919ebd2afe34eaf6078e4884ca575fa Mon Sep 17 00:00:00 2001 From: Matt Date: Thu, 23 Nov 2023 11:38:02 +0000 Subject: [PATCH] Un-excluded gnomad[eg]_nhomalt, and placed in correct position in column order --- egg5_config_v2.3.2.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/egg5_config_v2.3.2.py b/egg5_config_v2.3.2.py index ca97380..ff06ff3 100644 --- a/egg5_config_v2.3.2.py +++ b/egg5_config_v2.3.2.py @@ -72,7 +72,7 @@ "{}.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", @@ -80,7 +80,7 @@ "{}.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,