WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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c.921delA:p.D308Tfs*33 or *34 #146

Open worker000000 opened 3 years ago

worker000000 commented 3 years ago

Dear professor, Thanks a lot for making such a powerful sofeware, I have a variant in the following, the mutlyzer gives fs34, but the annovar gives fs33, this maybe caused by minor NM version , but table_annovar.pl does not support dbtype argument,can you have a look <> table_annovar.pl LX2007693_test.vardict.vcf annovar/humandb -buildver hg19 -out LX2007693.vardict.anno -remove -protocol refGene,1000g2015aug_all,clinvar_20210501,avsnp150,cosmic70 -operation g,f,f,f,f -argument '-hgvs,-hgvs,-hgvs,-hgvs,-hgvs' -nastring . -vcfinput -polish <> chr7 6027156 . CT C 160 PASS SAMPLE=LX2007693;TYPE=SNV;DP=31;END=2490898;VD=12;AF=0.3871;BIAS=2:2;REFBIAS=13:6;VARBIAS=7:5;PMEAN=22.4;PSTD=1;QUAL=44.9;QSTD=1;SBF=0.70543;ODDRATIO=1.52548;MQ=60;SN=24;HIAF=0.3871;ADJAF=0.0323;SHIFT3=0;MSI=4;MSILEN=1;NM=2.8;HICNT=12;HICOV=31;LSEQ=ACAGATGGGAAACCCGTTTG;RSEQ=GGGGTGGGTGTCTGGGTGGG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0;ANNOVAR_DATE=2018-04-16;Func.refGene=exonic;Gene.refGene=PMS2;GeneDetail.refGene=.;ExonicFunc.refGene=frameshift_deletion;AAChange.refGene=PMS2:NM_001322008:exon9:*c.921delA:p.D308Tfs33*,PMS2:NM_001322010:exon9:c.678delA:p.D227Tfs33,PMS2:NM_001322004:exon10:c.834delA:p.D279Tfs33,PMS2:NM_001322006:exon10:c.1083delA:p.D362Tfs33,PMS2:NM_001322007:exon10:c.921delA:p.D308Tfs33,PMS2:NM_001322013:exon10:c.666delA:p.D223Tfs33,PMS2:NM_000535:exon11:c.1239delA:p.D414Tfs33,PMS2:NM_001322003:exon11:c.834delA:p.D279Tfs33,PMS2:NM_001322005:exon11:c.834delA:p.D279Tfs33,PMS2:NM_001322009:exon11:c.834delA:p.D279Tfs33,PMS2:NM_001322011:exon11:c.306delA:p.D103Tfs33,PMS2:NM_001322012:exon11:c.306delA:p.D103Tfs33,PMS2:NM_001322014:exon11:c.1239delA:p.D414Tfs33,PMS2:NM_001322015:exon11:c.930delA:p.D311Tfs33;1000g2015aug_all=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;avsnp150=.;cosmic70=ID\x3dCOSM150905\x3bOCCURENCE\x3d1(stomach);ALLELE_END GT:DP:VD:AD:AF:RD:ALD 0/1:31:12:19,12:0.3871:13,6:7,5 <> <> https://mutalyzer.nl/name-checker?description=NM_001322008%3Ac.921delA image

worker000000 commented 3 years ago

there is another variant also seems to be also has something to do with NM minor version <> <> chr2 48030639 . AC A 166 f0.02 STATUS=LikelySomatic;SAMPLE=L2007450;TYPE=Deletion;DP=1513;VD=13;AF=0.0086;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.28503;SOR=2.66832;LSEQ=TAATTCTGTTGCCGGAAGAT;RSEQ=CCCCCCCTTCTTAGAGCTTA;ANNOVAR_DATE=2018-04-16;Func.refGene=exonic;Gene.refGene=MSH6;GeneDetail.refGene=.;ExonicFunc.refGene=frameshift_deletion;AAChange.refGene=MSH6:NM_001281492:exon3:c.2864delC:p.F958Sfs1,MSH6:NM_001281493:exon4:c.2348delC:p.F786Sfs1,*MSH6:NM_000179:exon5:c.3254delC:p.F1088Sfs1*,MSH6:NM_001281494:exon5:c.2348delC:p.F786Sfs1;1000g2015aug_all=.;CLNALLELEID=94837;CLNDN=Lynch-like_syndrome|Carcinoma_of_colon|Lynch_syndrome|Hereditary_cancer-predisposing_syndrome|Mismatch_repair_cancer_syndrome_3|Hereditary_nonpolyposis_colorectal_neoplasms|not_provided;CLNDISDB=.|MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0005835,MedGen:C4552100,OMIM:PS120435,Orphanet:ORPHA144|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0030841,MedGen:CN296221,OMIM:619097|MedGen:C0009405|MedGen:CN517202;CLNREVSTAT=reviewed_by_expert_panel;CLNSIG=Pathogenic;avsnp150=rs267608078;cosmic70=ID\x3dCOSM330655\x3bOCCURENCE\x3d7(large_intestine);ALLELE_END GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1513:13:5,8:653,847:1500,13:0.0086:2,2:30.5:1:45:0:0.78544:1.23336:60:26:0.0086:0:1 0/0:309:1:0,1:172,134:306,1:0.0032:2,0:32:0:37:0:0.43974:0:60:2:0.0033:0:0 <> <> https://mutalyzer.nl/name-checker?description=NM_000179%28MSH6_v001%29%3Ac.3254delC image