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Old 04-13-2016, 02:46 PM   #1
user 31888
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Join Date: Nov 2015
Posts: 19
Default VCF file missing GT field - How to fix?


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 \
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 !
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gtak, missing field, vcf file

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