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DiagnoseTargets: missing genotype field in output vcf


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 does not contain the GT field, which gives trouble after for annotating the vcc file.

Any workaround maybe?

Thanks !

Best Answer


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