You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
You are using VEP, not vcf2maf. But I'll try to help. If all the variants are showing as intergenic, then it is likely that you are using a transcript/reference that is a different human assembly than your VCF. E.g. hg19 VCF with hg38 VEP cache.
yes, I have tried to add the option to vcf2maf with the customed database which points to clinvar, but always failed. What is the best way to add the clinvar in vcf2maf?
I have vcf files which are generated using freebay, how could I add the clinvar annotation to the vcf and convert to maf?
I try to run as following
vep --input_file JH020.soma.freebayes.vcf --output_file JH020.soma.clinc.freebayes.vcf --format vcf --species homo_sapiens --custom /vep_ref/hg19/new/clinvar.vcf.gz,ClinVar,vcf,exact,0,CLNSIG,CLNREVSTAT,CLNSIGCONF
all the variant are intergenic_variant, which is not right
The text was updated successfully, but these errors were encountered: