i am running haplotypcaller in one bam file

dk86dk86 israelMember

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

Answers

Sign In or Register to comment.