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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

HaplotypeCaller does not work



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    Genevieve Brandt (she/her)

    Hi Roohollah kheiri,

    Thanks for writing into the forum so we can help to get HaplotypeCaller working for you! The error message with helpful information is here:

    java.lang.IllegalStateException: the sample list cannot be null or empty

    I think there is a problem in your input bam. Either you do not have read groups properly added, or the bam is not formatted correctly. Take a look at these resources:

    1. Validate that the bam file has correct formatting with the tool ValidateSamFile.
    2. Learn more about read groups & how to fix them.

    I hope this helps, please let me know if you have further questions.



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    Daniel Castañeda Mogollón

    Hello! I would like to follow up on this as I am getting the same error as well. Here's what I've done so far:

    Alignment of raw .fastq to a reference:

    bwa -mem 3d7_dhps.fasta R1.fastq R2.fastq > S13_dhps.sam

    Conversion from sam to bam:

    samtools view -b S13_dhps.sam > S13_dhps.bam


    samtools sort S13_dhps.bam > S13_dhps_sorted.bam

    Marking duplicates:

    picard MarkDuplicates -I S13_dhps_sorted.bam -O S13_marked_duplicates.bam -M S13_marked_duplicates_summary.txt

    Validating sam file:

    picard ValidateSamFile -I S13_dhps.bam -MODE SUMMARY

    Then I get this output, which I believe is the cause of my error message when I try running the HaplotypeCaller:

    ## HISTOGRAM java.lang.String

    Error Type Count



    For referencing I did this:

    samtools faidx 3d7_dhps.fasta

    And for the dictionary:

    gatk CreateSequenceDictionary -R 3d7_dhps.fasta


    I am a bit lost and desperate! Thanks for your help!

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    Genevieve Brandt (she/her)

    Daniel Castañeda Mogollón your issue looks different from this original post. It looks like you are having a problem with your read groups. If the linked article does not solve your issue, feel free to make a new post.

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    Daniel Castañeda Mogollón

    Yes! That fixed the issue! Thanks a lot!

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    Genevieve Brandt (she/her)

    Great, glad to hear it!

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