Please updata prepare_annovar_user.pl for clinvar_20240902.vcf.gz #254

xiucz · 2024-09-06T03:15:58Z

Dear Prof. Wang!

I try to update to ANNOVAR, but it gives error:

Error: invalid record found in avinputfile: <ALLELEID=3416616;CLNHGVS=NC_000001.10:g.2488139G>A;CLNVC=single_nucleotide_variant;CLNVCSO=SO:0001483;GENEINFO=TNFRSF14:8764|TNFRSF14-AS1:115110;MC=SO:0001587|nonsense;ONC=Likely_oncogenic;ONCDISDB=Human_Phenotype_Ontology:HP:0002664,Human_Phenotype_Ontology:HP:0003008,Human_Phenotype_Ontology:HP:0006741,MONDO:MONDO:0005070,MeSH:D009369,MedGen:C0027651;ONCDN=Neoplasm;ONCREVSTAT=criteria_provided,_single_submitter;ORIGIN=2
> at ..//prepare_annovar_user.pl line 301, <FH> line 9862.

Not every record has an CLNDN= tag. Could you update prepare_annovar_user.pl to handle the clinvar_20240902.vcf.gz?

Best,
xiucz

The text was updated successfully, but these errors were encountered:

ritayim2 · 2024-09-10T07:01:31Z

i also enounter the same issue. Can someone advise how to fix?

kaichop · 2024-09-23T13:55:22Z

The latest version of ClinVar adds two additional interpretations, ONC (oncogenecity) and SCI (somatic clinical impact). As a result, there will be more columns in the output file.

I have updated the prepare_annovar_user.pl file at http://www.openbioinformatics.org/annovar/download/prepare_annovar_user.pl

To run index_annovar.pl, you also need the comment file at http://www.openbioinformatics.org/annovar/download/comment_clinvar_20240917.txt

ClinVar also introduced the "included variants" in the new version. It is a bit confusing, but the explanation seems to be "Included variants: Classifications in ClinVar may be made for a single variant or a set of variants, such as a haplotype. Variants classified only as part of a set of variants (i.e. no direct classification for the variant itself) are considered "included" variants. The VCF files include both variants with a direct classification and included variants. Included variants do not have an associated disease (CLNDN, CLNDISDB) or a classification (CLNSIG). Instead, there are three INFO tags specific to included variants - CLNDNINCL, CLNDISDBINCL, and CLNSIGINCL (see below)." Based on such descriptions, the included variants should not be in the clinvar database in ANNOVAR and they will not be included.

xiucz · 2024-09-24T06:11:42Z

@kaichop

It appears that the bug is still present.Can you repeat it? Thanks a lot.

version=20240902
wget -c ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_${version}.vcf.gz
wget -c ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_${version}.vcf.gz.tbi
~/vt/vt decompose clinvar_${version}.vcf.gz -o temp.split.vcf
perl ..//prepare_annovar_user.pl_20240924 -dbtype clinvar_preprocess2 temp.split.vcf -out temp.split2.vcf

Error,

Error: invalid record found in avinputfile: <ALLELEID=3416616;CLNHGVS=NC_000001.10:g.2488139G>A;CLNVC=single_nucleotide_variant;CLNVCSO=SO:0001483;GENEINFO=TNFRSF14:8764|TNFRSF14-AS1:115110;MC=SO:0001587|nonsense;ONC=Likely_oncogenic;ONCDISDB=Human_Phenotype_Ontology:HP:0002664,Human_Phenotype_Ontology:HP:0003008,Human_Phenotype_Ontology:HP:0006741,MONDO:MONDO:0005070,MeSH:D009369,MedGen:C0027651;ONCDN=Neoplasm;ONCREVSTAT=criteria_provided,_single_submitter;ORIGIN=2
> at ..//prepare_annovar_user.pl_20240924 line 301, <FH> line 9862.

kaichop · 2024-09-24T13:37:56Z

I remember clinivar no longer uses multiallelic variants so this step is no longer needed. I just run 'vt decompose' myself and confirmed this (0 multiallelic variant). Therefore, you can just directly run prepare_annovar_user.pl -dbtype clinvar2 *input*.vcf -out hg38_clinvar_20240917_raw.txt I will update the documentation to reflect this.

…

On Tue, Sep 24, 2024 at 2:12 AM xiucz ***@***.***> wrote: @kaichop <https://github.com/kaichop> It appears that the bug is still present.Can you repeat it? Thanks a lot. version=20240902 wget -c ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_${version}.vcf.gz wget -c ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_${version}.vcf.gz.tbi ~/vt/vt <ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_$%7Bversion%7D.vcf.gz.tbi~/vt/vt> decompose clinvar_${version}.vcf.gz -o temp.split.vcf perl ..//prepare_annovar_user.pl_20240924 -dbtype clinvar_preprocess2 temp.split.vcf -out temp.split2.vcf Error, Error: invalid record found in avinputfile: <ALLELEID=3416616;CLNHGVS=NC_000001.10:g.2488139G>A;CLNVC=single_nucleotide_variant;CLNVCSO=SO:0001483;GENEINFO=TNFRSF14:8764|TNFRSF14-AS1:115110;MC=SO:0001587|nonsense;ONC=Likely_oncogenic;ONCDISDB=Human_Phenotype_Ontology:HP:0002664,Human_Phenotype_Ontology:HP:0003008,Human_Phenotype_Ontology:HP:0006741,MONDO:MONDO:0005070,MeSH:D009369,MedGen:C0027651;ONCDN=Neoplasm;ONCREVSTAT=criteria_provided,_single_submitter;ORIGIN=2 > at ..//prepare_annovar_user.pl_20240924 line 301, <FH> line 9862. — Reply to this email directly, view it on GitHub <#254 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OGIOHP5WM4B346USVTZYD7DJAVCNFSM6AAAAABNXWZW7SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZQGI3TOMRZGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

xiucz · 2024-09-26T23:10:02Z

It works now. Please keep this issue open for a while for newcomers who might encounter the same problem. Thank you.

kaichop · 2024-09-27T01:26:08Z

Thank you for letting me know.

…

On Thu, Sep 26, 2024 at 7:10 PM xiucz ***@***.***> wrote: It works now. Please keep this issue open for a while for newcomers who might encounter the same problem. Thank you. — Reply to this email directly, view it on GitHub <#254 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OG23MOOI4PAFVFMDWDZYSH6DAVCNFSM6AAAAABNXWZW7SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZYGA4TSMZTGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

ritayim2 · 2024-10-19T15:20:10Z

Dear Kai @kaichop,
Thanks a lot for updating. i tried the new script file for COSMIC100 cruated from Cosmic_GenomeScreensMutant_Vcf_v100_GRCh38.tar and Cosmic_GenomeScreensMutant_Tsv_v100_GRCh38.tar. For your information, the output file hg38_cosmic100.txt is 29837298 line as tutorial. However, I still encounter similar error and hope you or someone can advise on the issue:
prefield not defined (chr9 5022158 5022158 T A exonic JAK2 . nonsynonymous_SNV JAK2:NM_001322195:exon2:c.T171A:p.F57L,JAK2:NM_001322196:exon2:c.T171A:p.F57L,JAK2:NM_001322194:exon3:c.T171A:p.F57L,JAK2:NM_004972:exon3:c.T171A:p.F57L 9p24.1 . . . . . . . . . . . . . 0.313 0.13879 T 0.122 0.35710 T 0.012 0.16265 B 0.006 0.12133 B 0.000077 0.52346 D 0.137700 0.999386 0.46865 D 1.525 0.38595 L 0.87 0.46412 T -2.43 0.53258 N 0.549 0.57518 -1.0824 0.06890 T 0.065 0.26772 T 9 0.16422781 0.30730 T 0.008676 0.22927 T 0.127 0.34888 0.628 0.76366 0.5410184844 0.53754 0.4539470442581493 0.45312 0.213371676131 0.23852 0.609011411667 0.54175 T 0.616051 0.87899 D -0.299865 0.08672 T -0.404083 0.32910 T 0.0968818226698108 0.12010 T 0.79482 0.43725 T 0.4743418 0.65556 0.18350086 0.41343 0.4743418 0.65557 0.18350086 0.41342 -6.855 0.52967 T 0.3691061075986174 0.46481 0.877 0.81319 P .\x3b. .\x3b. 1.575725 0.20171 14.62 0.87117516596749178 0.17000 0.79197 0.39199 D AEFDBI 0.154525 0.27957 N -0.494471416308901 0.22260 1.187424 -0.380256747560047 0.25586 1.40798 0.891253416725197 0.25855 0.653281 0.48532 0 0.653731 0.59785 0 0.547309 0.15389 0 0.669 0.65921 0 . . 5.57 3.18 0.35615 1.125000 0.30946 . . 0.609000 0.47794 1.000000 0.71638 1.000000 0.68203 0.643000 0.32503 0.1318:0.1432:0.0:0.7249 5.189 0.14524 698 0.58074 FERM_domain|Band_4.1_domain\x3bFERM_domain|Band_4.1_domain . . . . . . . . . . . . 1.883e-05 0 0 0.0003 0 0 0 0 1.368e-06 1.368e-06 1.361e-06 1.375e-06 5.038e-05 2.3e-07 9e-08 8.35e-06 3.12e-06 0 0 0 5.038e-05 0 0 0 0 0 . . . 0.002959 . . chr9 5022158 . T A . PASS ADP=539;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR:AF 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/1:255:539:539:282:257:47.68%:8.9184E-96:35:32:98:184:100:157:0.476809 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. with field=408 and prefield=390 at /d1/software/annovar/table_annovar.pl line 186, line 9.

kaichop · 2024-10-19T15:26:02Z

Did you follow instructions exactly? https://annovar.openbioinformatics.org/en/latest/user-guide/filter/ tar xvf Cosmic_GenomeScreensMutant_Vcf_v100_GRCh38.tartar xvf Cosmic_GenomeScreensMutant_Tsv_v100_GRCh38.targunzip Cosmic_GenomeScreensMutant_v100_GRCh38.vcf.gzgunzip Cosmic_GenomeScreensMutant_v100_GRCh38.tsv.gztar xvf Cosmic_NonCodingVariants_Tsv_v100_GRCh38.tartar xvf Cosmic_NonCodingVariants_Vcf_v100_GRCh38.targunzip Cosmic_NonCodingVariants_v100_GRCh38.vcf.gzgunzip Cosmic_NonCodingVariants_v100_GRCh38.tsv.gzecho -e '#Chr\tStart\tEnd\tRef\tAlt\tCOSMIC100' > hg38_cosmic100_raw.txtprepare_annovar_user.pl -dbtype cosmic Cosmic_GenomeScreensMutant_v100_GRCh38.tsv -vcf Cosmic_GenomeScreensMutant_v100_GRCh38.vcf >> hg38_cosmic100_raw.txt prepare_annovar_user.pl -dbtype cosmic Cosmic_NonCodingVariants_v100_GRCh38.tsv -vcf Cosmic_NonCodingVariants_v100_GRCh38.vcf >> hg38_cosmic100_raw.txt index_annovar.pl hg38_cosmic100_raw.txt -outfile hg38_cosmic100.txt wc -l hg38_cosmic100.txt29837298 hg38_cosmic100.txt

…

On Sat, Oct 19, 2024 at 11:20 AM Rita Lok Hay Yim ***@***.***> wrote: i also enounter the same issue. Can someone advise how to fix? sorry i tried the new script file for COSMIC100 but I still encounter similar error: prefield not defined (chr9 5022158 5022158 T A exonic JAK2 . nonsynonymous_SNV JAK2:NM_001322195:exon2:c.T171A:p.F57L,JAK2:NM_001322196:exon2:c.T171A:p.F57L,JAK2:NM_001322194:exon3:c.T171A:p.F57L,JAK2:NM_004972:exon3:c.T171A:p.F57L 9p24.1 . . . . . . . . . . . . . 0.313 0.13879 T 0.122 0.35710 T 0.012 0.16265 B 0.006 0.12133 B 0.000077 0.52346 D 0.137700 0.999386 0.46865 D 1.525 0.38595 L 0.87 0.46412 T -2.43 0.53258 N 0.549 0.57518 -1.0824 0.06890 T 0.065 0.26772 T 9 0.16422781 0.30730 T 0.008676 0.22927 T 0.127 0.34888 0.628 0.76366 0.5410184844 0.53754 0.4539470442581493 0.45312 0.213371676131 0.23852 0.609011411667 0.54175 T 0.616051 0.87899 D -0.299865 0.08672 T -0.404083 0.32910 T 0.0968818226698108 0.12010 T 0.79482 0.43725 T 0.4743418 0.65556 0.18350086 0.41343 0.4743418 0.65557 0.18350086 0.41342 -6.855 0.52967 T 0.3691061075986174 0.46481 0.877 0.81319 P .\x3b. .\x3b. 1.575725 0.20171 14.62 0.87117516596749178 0.17000 0.79197 0.39199 D AEFDBI 0.154525 0.27957 N -0.494471416308901 0.22260 1.187424 -0.380256747560047 0.25586 1.40798 0.891253416725197 0.25855 0.653281 0.48532 0 0.653731 0.59785 0 0.547309 0.15389 0 0.669 0.65921 0 . . 5.57 3.18 0.35615 1.125000 0.30946 . . 0.609000 0.47794 1.000000 0.71638 1.000000 0.68203 0.643000 0.32503 0.1318:0.1432:0.0:0.7249 5.189 0.14524 698 0.58074 FERM_domain|Band_4.1_domain\x3bFERM_domain|Band_4.1_domain . . . . . . . . . . . . 1.883e-05 0 0 0.0003 0 0 0 0 1.368e-06 1.368e-06 1.361e-06 1.375e-06 5.038e-05 2.3e-07 9e-08 8.35e-06 3.12e-06 0 0 0 5.038e-05 0 0 0 0 0 . . . 0.002959 . . chr9 5022158 . T A . PASS ADP=539;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR:AF 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/1:255:539:539:282:257:47.68%:8.9184E-96:35:32:98:184:100:157:0.476809 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. with field=408 and prefield=390 at /d1/software/annovar/table_annovar.pl line 186, line 9. — Reply to this email directly, view it on GitHub <#254 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OF3HFMEAS6FN34E263Z4J2D7AVCNFSM6AAAAABNXWZW7SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRTHE3DCNZZGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

kaichop · 2024-10-19T15:27:25Z

what do you mean "I still encounter similar error"? did not you already generate the correct file with the correct number of lines?

…

On Sat, Oct 19, 2024 at 11:25 AM Rita Lok Hay Yim ***@***.***> wrote: Dear Kai @kaichop <https://github.com/kaichop>, Thanks a lot for updating. i tried the new script file for COSMIC100 cruated from Cosmic_GenomeScreensMutant_Vcf_v100_GRCh38.tar and Cosmic_GenomeScreensMutant_Tsv_v100_GRCh38.tar. For your information, the output file hg38_cosmic100.txt is 29837298 line as tutorial. However, I still encounter similar error and hope you or someone can advise on the issue: prefield not defined (chr9 5022158 5022158 T A exonic JAK2 . nonsynonymous_SNV JAK2:NM_001322195:exon2:c.T171A:p.F57L,JAK2:NM_001322196:exon2:c.T171A:p.F57L,JAK2:NM_001322194:exon3:c.T171A:p.F57L,JAK2:NM_004972:exon3:c.T171A:p.F57L 9p24.1 . . . . . . . . . . . . . 0.313 0.13879 T 0.122 0.35710 T 0.012 0.16265 B 0.006 0.12133 B 0.000077 0.52346 D 0.137700 0.999386 0.46865 D 1.525 0.38595 L 0.87 0.46412 T -2.43 0.53258 N 0.549 0.57518 -1.0824 0.06890 T 0.065 0.26772 T 9 0.16422781 0.30730 T 0.008676 0.22927 T 0.127 0.34888 0.628 0.76366 0.5410184844 0.53754 0.4539470442581493 0.45312 0.213371676131 0.23852 0.609011411667 0.54175 T 0.616051 0.87899 D -0.299865 0.08672 T -0.404083 0.32910 T 0.0968818226698108 0.12010 T 0.79482 0.43725 T 0.4743418 0.65556 0.18350086 0.41343 0.4743418 0.65557 0.18350086 0.41342 -6.855 0.52967 T 0.3691061075986174 0.46481 0.877 0.81319 P .\x3b. .\x3b. 1.575725 0.20171 14.62 0.87117516596749178 0.17000 0.79197 0.39199 D AEFDBI 0.154525 0.27957 N -0.494471416308901 0.22260 1.187424 -0.380256747560047 0.25586 1.40798 0.891253416725197 0.25855 0.653281 0.48532 0 0.653731 0.59785 0 0.547309 0.15389 0 0.669 0.65921 0 . . 5.57 3.18 0.35615 1.125000 0.30946 . . 0.609000 0.47794 1.000000 0.71638 1.000000 0.68203 0.643000 0.32503 0.1318:0.1432:0.0:0.7249 5.189 0.14524 698 0.58074 FERM_domain|Band_4.1_domain\x3bFERM_domain|Band_4.1_domain . . . . . . . . . . . . 1.883e-05 0 0 0.0003 0 0 0 0 1.368e-06 1.368e-06 1.361e-06 1.375e-06 5.038e-05 2.3e-07 9e-08 8.35e-06 3.12e-06 0 0 0 5.038e-05 0 0 0 0 0 . . . 0.002959 . . chr9 5022158 . T A . PASS ADP=539;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR:AF 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/1:255:539:539:282:257:47.68%:8.9184E-96:35:32:98:184:100:157:0.476809 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. 0/0:.:.:.:.:.:.:.:.:.:.:.:.:.:. with field=408 and prefield=390 at /d1/software/annovar/table_annovar.pl line 186, line 9. — Reply to this email directly, view it on GitHub <#254 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OABDDZPSL37LUNTTGLZ4J2XFAVCNFSM6AAAAABNXWZW7SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRTHE3DCNZZGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

ritayim2 · 2024-10-19T15:33:50Z

Thank you for your fast response, I did successfully generated hg38_cosmic100.txt with the same number of lines as your instruction. Just when I run the ANNOVAR to annotate my vcf, I get an error which casued premature termination of the process. saying the one of the variant that my in vcf has "prefield not defined"
However i don't see this error when I re-run the same VCF with my old hg38_cosmic98_coding.txt

kaichop · 2024-10-19T15:50:38Z

so do you mean you have a problem when annotating a mutation " chr9 5022158", not that you have a problem generating the cosmic annotation database using prepare_annovar_user? Can you try use only the cosmic database in the annotation (it seems that you have many columns in the output) to insulate the problem to be for this particular mutation for this particular annotation dbtype?

…

On Sat, Oct 19, 2024 at 11:34 AM Rita Lok Hay Yim ***@***.***> wrote: Thank you for your fast response, I did successfully generated hg38_cosmic100.txt with the same number of lines as your instruction. Just when I run the ANNOVAR to annotate my vcf, I get an error which casued premature termination of the process. saying the one of the variant that my in vcf has "prefield not defined" However i don't see this error when I re-run the same VCF with my old hg38_cosmic98_coding.txt — Reply to this email directly, view it on GitHub <#254 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OASD4FY34YB2YJ4PQDZ4J3XHAVCNFSM6AAAAABNXWZW7SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRTHE3TMMZWGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

ritayim2 · 2024-10-19T16:05:42Z

Yes. you are correct I have problem annotating one line of variants. I just retried using just refGene and COSMIC and i still get the error. My many columns comes from the FORMAT field which is a multi-sample vcf with around 15 subfields.

Interestingly, I notice the line after this failing line is a variant that COSMIC100 has entry. And the information has spanned to other colmuns (I have uploaded here for your reference).
dummy.hg38_multianno.txt

lincj1994 · 2024-11-13T06:28:19Z

Hi @xiucz .
I encountered a similar error #264. I'm wondering if you can help resolve this error or share your code.
Many thanks!

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Please updata prepare_annovar_user.pl for clinvar_20240902.vcf.gz #254

Please updata prepare_annovar_user.pl for clinvar_20240902.vcf.gz #254

xiucz commented Sep 6, 2024

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Please updata prepare_annovar_user.pl for clinvar_20240902.vcf.gz #254

Please updata prepare_annovar_user.pl for clinvar_20240902.vcf.gz #254

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ritayim2 commented Oct 19, 2024 • edited Loading

kaichop commented Oct 19, 2024 via email

kaichop commented Oct 19, 2024 via email

ritayim2 commented Oct 19, 2024

kaichop commented Oct 19, 2024 via email

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lincj1994 commented Nov 13, 2024

ritayim2 commented Oct 19, 2024 •

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