VCF file missing GT field - How to fix?

[user 31888]

Hi,

I am using GATK DiagnoseTargets to get some stats about the coverage of my reads compared to an exome interval list.

For that, I am running the following command:

${java} -jar ${GATK} \
   -T DiagnoseTargets \
   -R human_g1k_v37.fasta \
   -L truseq_interval.bed \
   -ip 100 \
   -I cleaned.bam \
   -o interval_stats.vcf \
   -writeFullFormat

It works great except that the output .vcf file does not contain the GT field.

This is a problem when running Annovar farther for annotating the vcf file.
I get this error message with Annovar:

Error: invalid record in VCF file: the GT specifier is not present in the FORMAT string

Any workaround maybe for adding the GT field?

Thanks !