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:
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:
Any workaround maybe for adding the GT field?
Thanks !
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:
Code:
${java} -jar ${GATK} \ -T DiagnoseTargets \ -R human_g1k_v37.fasta \ -L truseq_interval.bed \ -ip 100 \ -I cleaned.bam \ -o interval_stats.vcf \ -writeFullFormat
This is a problem when running Annovar farther for annotating the vcf file.
I get this error message with Annovar:
Code:
Error: invalid record in VCF file: the GT specifier is not present in the FORMAT string
Thanks !