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GVCF error - Argument emitRefConfidence has a bad value

I have run the following command on a small number of samples using a script with GATK (version 3.1-1-g07a4bf8).

java -Xmx8G -jar ${gatk_dir}/GenomeAnalysisTK.jar -R ${ref_dir}/${genome} \
-T HaplotypeCaller \
-I ${in_dir}/"36E_"${REGION}""${SAMPLE_ABB}"_lowqNrecalibrated_3.bam" \
--min_base_quality_score 30 \
--emitRefConfidence GVCF \
--variant_index_type LINEAR \
--variant_index_parameter 128000 \
--intervals $sites_dir/$file \
-o ${out_dir}/"37F
"${REGION}"_"${SAMPLE_ABB}"_HapCal_gVCF.vcf" \

It ran fine for all but one of the samples where I got this error

Invalid command line: Argument emitRefConfidence has a bad value: Can only be used in single sample mode currently

I found that there was a typo in my read groups which made it appear the bam was from two samples not one. I fixed this by converting bam to sam, then using sed to rename the readgroup sample name, then sam to bam and reindex. But the error is still happening.
Does anyone have any ideas about what to try next to fix this?


Best Answer


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