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I used these two commands to annotate my vcf file (VarDict) with information from dbSNP and from clinvar. With dbSNP, resulting file contained SNP information in both ID and INFO columns. Using clinvar I got annotation only in ID column, no information from clinvar.vcf was transferred to INFO column. In both cases "SnpSift.jar annotate -id" and "SnpSift.jar annotate" had the same results. Results, therefore, depended on file used to annotate and did not depended on the command used. My commands:
java -jar /data/home/"$USER"/snpEff/SnpSift.jar annotate -id /data/amplicon_ref/GCF_000001405.39_P_Genes.vcf.gz MH2021102901.CDS.vcf > MH2021102901.CDS.Sift.SNP.vcf
java -jar /data/home/"$USER"/snpEff/SnpSift.jar annotate -id clinvar_20220528.vcf MH2021102901.CDS.vcf > MH2021102901.CDS.Sift.clin.vcf
and two other commands that omitted "-id"
Both dbSNP and clinvar input files were modified to contain the same type of names (chr1, chr2, ...) for chromosomes to match my VarDict vcf file. In dbSNP file I kept only SNPs located in regions where mutations were called by VarDict.
Thank you, Jiri
The text was updated successfully, but these errors were encountered:
I used these two commands to annotate my vcf file (VarDict) with information from dbSNP and from clinvar. With dbSNP, resulting file contained SNP information in both ID and INFO columns. Using clinvar I got annotation only in ID column, no information from clinvar.vcf was transferred to INFO column. In both cases "SnpSift.jar annotate -id" and "SnpSift.jar annotate" had the same results. Results, therefore, depended on file used to annotate and did not depended on the command used. My commands:
java -jar /data/home/"$USER"/snpEff/SnpSift.jar annotate -id /data/amplicon_ref/GCF_000001405.39_P_Genes.vcf.gz MH2021102901.CDS.vcf > MH2021102901.CDS.Sift.SNP.vcf
java -jar /data/home/"$USER"/snpEff/SnpSift.jar annotate -id clinvar_20220528.vcf MH2021102901.CDS.vcf > MH2021102901.CDS.Sift.clin.vcf
and two other commands that omitted "-id"
Both dbSNP and clinvar input files were modified to contain the same type of names (chr1, chr2, ...) for chromosomes to match my VarDict vcf file. In dbSNP file I kept only SNPs located in regions where mutations were called by VarDict.
Thank you, Jiri
The text was updated successfully, but these errors were encountered: