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i am running haplotypcaller in one bam file
java -jar GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T HaplotypeCaller -R reference/GRCh37/hs37d5.fa -I output.bam --dbsnp reference/gatkbundle/dbsnp_138.b37.vcf -o output.g.vcf -ERC GVCF
i am trying add one more bam file to my cohort. i ran one bam file separately, but while applying gvcf mode it is not running . it is throwing the below error.
MESSAGE: Invalid command line: Argument emitRefConfidence has a bad value: Can only be used in single sample mode currently. Use the sample_name argument to run on a single sample out of a multi-sample BAM file