Errors about read group (RG) information

delangeldelangel Posts: 71GATK Dev mod
edited November 20 in Common Problems

What are read groups?

See the Dictionary entry on read groups.

Errors about missing or undefined read groups

As detailed in the FAQs about input requirements, GATK expects all read groups appearing in the read data to be specified in the file header, and will fail with an error if it does not find that information (whether there is no read group information in the file, or a subset of reads do not have read groups).


You can use a Picard tool called AddOrReplaceReadGroups to add the missing information to your input file.

Here's an example:

# throws an error
java -jar GenomeAnalysisTK.jar \
    -T HaplotypeCaller \
    -R reference.fasta \
    -I reads_without_RG.bam \
    -o output.vcf

# fix the read groups
java -jar picard.jar AddOrReplaceReadGroups \
    I= reads_without_RG.bam \
    O=  reads_with_RG.bam \
    SORT_ORDER=coordinate \
    RGID=foo \
    RGLB=bar \
    RGPL=illumina \
    RGSM=Sample1 \

# runs without error
java -jar GenomeAnalysisTK.jar \
    -T HaplotypeCaller \
    -R reference.fasta \
    -I reads_with_RG.bam \
    -o output.vcf

Note that if you don't know what information to put in the read groups, you should ask whoever performed the sequencing or provided the BAM to give you the metadata you need.

Post edited by Geraldine_VdAuwera on
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