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mskcc / vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
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how to run vcf2maf with clinvar db #327

Open songeric1107 opened 2 years ago

songeric1107 commented 2 years ago

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

ckandoth commented 2 years ago

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.

songeric1107 commented 2 years ago

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?