ANNOVAR annotation

Question

[Eliza]

Hi,

I'm trying to annotate VCF file:

I run the following command

table_annovar.pl \
  --vcfinput eczema.vcf \
  humandb/ \
  -buildver hg19 \
  -out ecze \
  -remove \
  -protocol refGene,cytoBand,exac03,avsnp147,dbnsfp30a \
  -operation g,r,f,f,f \
  -nastring . \
  -polish

but I get the following error :

NOTICE: Running with system command <convert2annovar.pl  -includeinfo -allsample -withfreq -format vcf4 eczema.vcf > ecze.avinput >
Error: invalid record in VCF file: the GT specifier is not present in the FORMAT string: < 1       754182       .       A       G   .> 
Error running system command: <convert2annovar.pl  -includeinfo -allsample -withfreq -format vcf4 eczema.vcf > ecze.avinput>

I can't seem to understand what is the error would be happy for help

Answer 1

[Pierre Lindenbaum]

: the GT specifier is not present in the FORMAT string

The is a FORMAT column. When this column exists, a VCF is expected to have some other columns for the genotypes.

The following column could fix the problem.

cut -f1-8 < eczema.vcf > new.vcf

and test with 'new.vcf'