Here, I've got a VCF file I want to convert to ANNOVAR format through running the following command, but apparently it is not working!
table_annovar.pl 1_23_intersect.vcf /scratch/GENE_DATABASES/humandb/HG19_APR13/ -protocol refGene,phastConsElements44way,genomicSuperDups,esp6500si_all,1000g2012apr_all,snp135,ljb_all -operation g,r,r,f,f,f,f -vcfinput .
I was wondering if anyone has any suggestion on how to sort this out.
Could you solve the issue? Even I am facing the same problem. Everytime I use this
table_annovar.pl, I get an error, saying its a syntax issue.