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marc-sturmmarc-sturm
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updated test data (bug fix in VcfAnnotateMaxEntScan)
1 parent 24d1e0b commit eb81c57

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‎settings_nightly.ini

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@@ -38,7 +38,7 @@ container_methylartist = v1.3.1
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container_minimap2 = v2.28
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container_modkit = v0.3.2
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container_msisensor-pro = v1.2.0
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container_ngs-bits = 2025-03
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container_ngs-bits = master-2025-03-5-gbdce43fe
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container_orad = v2.6.1
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container_paraphase = v3.2.1
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container_python = v3.10.9

‎test/data/an_vep_out1.vcf

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‎test/data/an_vep_out2.vcf

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‎test/data/an_vep_out3.vcf

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@@ -91,8 +91,8 @@
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##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
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##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878_03
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chr1 179366128 . T TC 1259 . MQM=60;SAP=7;ABP=3;CSQ=C|intron_variant|ENST00000367618.8|Transcript||rs112230056|protein_coding|,C|intron_variant|ENST00000617277.4|Transcript||rs112230056|protein_coding|,C|regulatory_region_variant|ENSR00001303928|RegulatoryFeature||rs112230056|open_chromatin_region|,C|TF_binding_site_variant|ENSM00524779683|MotifFeature||rs112230056||,C|TF_binding_site_variant|ENSM00523262936|MotifFeature||rs112230056||;CSQ2=C|intron_variant|MODIFIER|AXDND1|HGNC:26564|ENST00000617277.4|Transcript||1/24|c.-107+128_-107+129insC|,C|intron_variant|MODIFIER|AXDND1|HGNC:26564|ENST00000367618.8|Transcript||1/25|c.-107+128_-107+129insC|;MES_SWA=9.3&2.5&9.3&0.0&0.0&-0.7&ENST00000617277|9.3&2.5&9.3&0.0&0.0&-0.7&ENST00000367618;gnomADg_AC=2;gnomADg_AF=0.00007;gnomADg_Hom=0;gnomADg_Hemi=.;gnomADg_Het=2;gnomADg_Wt=27652;gnomADg_AFR_AF=0.00038;gnomADg_AMR_AF=0.00000;gnomADg_EAS_AF=0.00000;gnomADg_NFE_AF=0.00000;gnomADg_SAS_AF=0.00000;CADD_INDEL=3.768;SpliceAI=TC|AXDND1|0.00|0.00|0.00|0.00|44|12|-43|-2;NGSD_GENE_INFO=AXDND1%20(inh%3DAR%20oe_syn%3D0.99%20oe_mis%3D1.04%20oe_lof%3D0.78) GT:DP:AO:GQ 0/1:103:50:160
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chr1 179366129 . A G 1259 . MQM=60;SAP=7;ABP=3;CSQ=G|intron_variant|ENST00000367618.8|Transcript||rs56018642|protein_coding|,G|intron_variant|ENST00000617277.4|Transcript||rs56018642|protein_coding|,G|regulatory_region_variant|ENSR00001303928|RegulatoryFeature||rs56018642|open_chromatin_region|,G|TF_binding_site_variant|ENSM00524779683|MotifFeature||rs56018642||,G|TF_binding_site_variant|ENSM00523262936|MotifFeature||rs56018642||;CSQ2=G|intron_variant|MODIFIER|AXDND1|HGNC:26564|ENST00000617277.4|Transcript||1/24|c.-107+129A>G|,G|intron_variant|MODIFIER|AXDND1|HGNC:26564|ENST00000367618.8|Transcript||1/25|c.-107+129A>G|;PHYLOP=0.463;MES_SWA=9.3&5.3&9.3&0.0&0.2&-1.7&ENST00000617277|9.3&5.3&9.3&0.0&0.2&-1.7&ENST00000367618;CADD_SNV=9.360;SpliceAI=G|AXDND1|0.00|0.00|0.00|0.00|43|11|-44|-3;NGSD_GENE_INFO=AXDND1%20(inh%3DAR%20oe_syn%3D0.99%20oe_mis%3D1.04%20oe_lof%3D0.78) GT:DP:AO:GQ 0/1:103:50:160
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chr1 179366128 . T TC 1259 . MQM=60;SAP=7;ABP=3;CSQ=C|intron_variant|ENST00000367618.8|Transcript||rs112230056|protein_coding|,C|intron_variant|ENST00000617277.4|Transcript||rs112230056|protein_coding|,C|regulatory_region_variant|ENSR00001303928|RegulatoryFeature||rs112230056|open_chromatin_region|,C|TF_binding_site_variant|ENSM00524779683|MotifFeature||rs112230056||,C|TF_binding_site_variant|ENSM00523262936|MotifFeature||rs112230056||;CSQ2=C|intron_variant|MODIFIER|AXDND1|HGNC:26564|ENST00000617277.4|Transcript||1/24|c.-107+128_-107+129insC|,C|intron_variant|MODIFIER|AXDND1|HGNC:26564|ENST00000367618.8|Transcript||1/25|c.-107+128_-107+129insC|;MES_SWA=9.3&2.5&9.3&0.0&0.0&0.0&ENST00000617277|9.3&2.5&9.3&0.0&0.0&0.0&ENST00000367618;gnomADg_AC=2;gnomADg_AF=0.00007;gnomADg_Hom=0;gnomADg_Hemi=.;gnomADg_Het=2;gnomADg_Wt=27652;gnomADg_AFR_AF=0.00038;gnomADg_AMR_AF=0.00000;gnomADg_EAS_AF=0.00000;gnomADg_NFE_AF=0.00000;gnomADg_SAS_AF=0.00000;CADD_INDEL=3.768;SpliceAI=TC|AXDND1|0.00|0.00|0.00|0.00|44|12|-43|-2;NGSD_GENE_INFO=AXDND1%20(inh%3DAR%20oe_syn%3D0.99%20oe_mis%3D1.04%20oe_lof%3D0.78) GT:DP:AO:GQ 0/1:103:50:160
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chr1 179366129 . A G 1259 . MQM=60;SAP=7;ABP=3;CSQ=G|intron_variant|ENST00000367618.8|Transcript||rs56018642|protein_coding|,G|intron_variant|ENST00000617277.4|Transcript||rs56018642|protein_coding|,G|regulatory_region_variant|ENSR00001303928|RegulatoryFeature||rs56018642|open_chromatin_region|,G|TF_binding_site_variant|ENSM00524779683|MotifFeature||rs56018642||,G|TF_binding_site_variant|ENSM00523262936|MotifFeature||rs56018642||;CSQ2=G|intron_variant|MODIFIER|AXDND1|HGNC:26564|ENST00000617277.4|Transcript||1/24|c.-107+129A>G|,G|intron_variant|MODIFIER|AXDND1|HGNC:26564|ENST00000367618.8|Transcript||1/25|c.-107+129A>G|;PHYLOP=0.463;MES_SWA=9.3&5.3&9.3&0.0&0.2&0.0&ENST00000617277|9.3&5.3&9.3&0.0&0.2&0.0&ENST00000367618;CADD_SNV=9.360;SpliceAI=G|AXDND1|0.00|0.00|0.00|0.00|43|11|-44|-3;NGSD_GENE_INFO=AXDND1%20(inh%3DAR%20oe_syn%3D0.99%20oe_mis%3D1.04%20oe_lof%3D0.78) GT:DP:AO:GQ 0/1:103:50:160
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chr22 10678964 . A G 199 low_conf_region MQM=21;SAP=7;ABP=3;CSQ=G|regulatory_region_variant|ENSR00000300759|RegulatoryFeature||rs1322557233|CTCF_binding_site|,G|regulatory_region_variant|ENSR00000665475|RegulatoryFeature||rs1322557233|open_chromatin_region|,G|intergenic_variant||||rs1322557233||;CSQ2=G|intergenic_variant|MODIFIER||||||||;PHYLOP=1.766;gnomADg_AC=38197;gnomADg_AF=0.43264;gnomADg_Hom=3454;gnomADg_Hemi=.;gnomADg_Het=31289;gnomADg_Wt=50091;gnomADg_AFR_AF=0.31676;gnomADg_AMR_AF=0.42116;gnomADg_EAS_AF=0.37467;gnomADg_NFE_AF=0.49959;gnomADg_SAS_AF=0.43106;CADD_SNV=12.85 GT:DP:AO:GQ 0/1:50:25:160
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chr22 10678984 . G T 167 low_conf_region MQM=21;SAP=4;ABP=3;CSQ=T|regulatory_region_variant|ENSR00000300759|RegulatoryFeature||rs1458164446|CTCF_binding_site|,T|regulatory_region_variant|ENSR00000665475|RegulatoryFeature||rs1458164446|open_chromatin_region|,T|intergenic_variant||||rs1458164446||;CSQ2=T|intergenic_variant|MODIFIER||||||||;PHYLOP=4.561;gnomADg_AC=45906;gnomADg_AF=0.48099;gnomADg_Hom=4714;gnomADg_Hemi=.;gnomADg_Het=36478;gnomADg_Wt=49534;gnomADg_AFR_AF=0.37532;gnomADg_AMR_AF=0.47043;gnomADg_EAS_AF=0.42588;gnomADg_NFE_AF=0.53908;gnomADg_SAS_AF=0.47109;CADD_SNV=17.47 GT:DP:AO:GQ 0/1:44:21:138
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chr22 10703585 . G A 1069 . MQM=33;SAP=3;ABP=175;CSQ=A|intergenic_variant||||rs1232560778||;CSQ2=A|intergenic_variant|MODIFIER||||||||;PHYLOP=-1.795;gnomADg_AC=62142;gnomADg_AF=0.48225;gnomADg_Hom=154;gnomADg_Hemi=.;gnomADg_Het=61834;gnomADg_Wt=66716;gnomADg_AFR_AF=0.46285;gnomADg_AMR_AF=0.48572;gnomADg_EAS_AF=0.46116;gnomADg_NFE_AF=0.49221;gnomADg_SAS_AF=0.48353;CADD_SNV=0.004 GT:DP:AO:GQ 0/1:361:96:160

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