Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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


Sign In or Register to comment.