SNV annotation with ANNOVAR to attach eQTL

Hi All,

I want to annotate my SNVs with eQTL, how to build the customed database?

BTW, my current ANNOVAR annotation line is:

table_annovar.pl ../annovar/chr22.dose.vcf.avinput  ~/hpc/tools/annovar/humandb/ --thread 4 -buildver hg19 --csvout -out ../annovar/chr22 -remove -protocol refGene,cytoBand,exac03,dbnsfp30a,gwasCatalog,wgRna,targetScanS,tfbsConsSites -operation gx,r,f,f,r,r,r,r -nastring . -otherinfo -polish -xref ~/hpc/tools/annovar/humandb/gene_fullxref.txt

Thansk.

snv eqtl annovar

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written 7.8 years ago by Shicheng Guo

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