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BAMs with multiple RG lines

5581681555816815 TNMember
edited November 2016 in Ask the GATK team


I have a set of BAMs, of them most contains multiple RG lines (same sample were run multiple times sequencing).

Now I need to run GATK HC caller (the BAM-> g.vcf -> vcf route), it complains that:

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.

The command I used:
java -XX:ParallelGCThreads=4 -Xms10g -Xmx10g -Djava.io.tmpdir=/scratch_space \
-jar GenomeAnalysisTK.jar -T HaplotypeCaller \
-R GRCh37-lite.fa --emitRefConfidence GVCF \
--variant_index_type LINEAR --variant_index_parameter 128000 \
--dbsnp dbsnp_138.b37.vcf -I input.bam -L 4 \
-o output.chr4.g.vcf

I am guessing if I provide the following parameter it will run the that sample ONLY?

What would be the easiest way to get around this? I know that I can

  • use picard to modify the RG tag, generating new BAMs
  • any other ways to get haplotypecaller run?


Post edited by 55816815 on


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