I an new to WGS analysis, i am trying to run haplotypecaller in one bam file.
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R GRCh37/hs37d5.fa -I LG_GWG.1.bam -D reference/gatkbundle/dbsnp_138.b37.vcf -o LG_GWG.output.g.vcf -ERC GVCF -nct 4
can anyone help me to figure out this issue. thanks
the error that put out :
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