Hello, I tried to convert my raw unfiltered Deepvariant vcf samples to Annovar format. First, I runned script with hg19 build, but got this error
WARNING: 1884 exonic SNPs have WRONG reference alleles specified in your input file! WARNING: An example input line is <chr11 11964514 11964514 T C hom 54.5 171 chr11 11964514 . T C 54.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:54:171:0,171:1:54,62,0> WARNING: ANNOVAR can still annotate exonic_variant_function for the mutation correctly! WARNING: you may have used wrong -buildver, or specified incorrect reference allele, or used outdated mRNA FASTA file!
I switched to hg38 build, so I downloaded additional packages. Then I got this error message
A total of 27174 sequences cannot be found in humandb/hg38_refGeneMrna.fa
here is my command line
./convert2annovar.pl -format vcf4 $file -outfile $outfile -includeinfo -withzyg -withfreq
So which reference genome should I use then? Or there are certain file types I can only use for Annovar?