Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

A USER ERROR has occurred: Number of read groups must be >= 1, but is 0

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    Tiffany Miller

    Hi Jay Singh ,

    You are getting this issue because the tool isn't finding any read groups in your input BAM. The recalibration system is read-group aware and you can read more about its importance here. When you run this command on your input BAM, what is the result:

    samtools view -H sample.bam | grep '@RG'
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    Jay Singh

    Thanks for the reply.

    When I ran the following command, I didn't got any output.

    samtools view -H sample.bam | grep '@RG'

    I have used the following command to add groups into my BAM file.

    java -jar picard.jar AddOrReplaceReadGroups \
    I= /home/deepak/NEW_SAMPLE/sample3Ncigar.bam \
    O= sample3_RG1.bam \
    RGID=1 \
    RGLB=lib2 \
    RGPL=illumina \
    RGPU=unit1 \
    RGSM=3

    Is it a correct way to do?

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    Tiffany Miller

    Using AddOrReplaceReadGroups to add your read group information fields so the @RG ID is unique per sample per lane is a way to do it, yes! Were you able to run BaseRecalibrator afterward with no issue?

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    Jay Singh

    Thanks for the reply.

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