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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

ASEReadCounter outputting blank table

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    Anthony Dias-Ciarla

    Hi Leslie Youtsey,

    Thank you for writing to the GATK forum. I hope that we can help you sort this out.

    Our developers noticed that ASEReadCounter likely failed because the BAM does not specify a read group. You populated the read groups with AddOrReplaceReadGroups before proceeding to count them. You seem to be using the original BAM as input to ASEReaderCounter, rather than the newly generated BAM with the read groups.

    In the final step, the input BAM should be:

    /ches/data10/lgspeight/results/Align/A_1_32.2.bam

    not,

    /ches/data10/lgspeight/results/Align/A_1_32.bam

    Please let me know if this helps! Feel free to reach out with any further questions.

    Best,
    Anthony

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    Leslie Youtsey

    That did the trick! Thanks Anthony Dias-Ciarla. Sometimes it just takes a second eye to catch the small things. 

    The table output looks good! But I have a second questions. In the table is the contig and position of the SNP, but I would like to add the gene or feature that the SNP is within. This would involve the gff annotation file. Do you know of a tool that GATK offers that could add this to the table? 

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    Anthony Dias-Ciarla

    Hi Leslie Youtsey,

    Thank you so much for following up! Yes, sometimes all we need is an extra set of eyes in these circumstances.

    Regarding your inquiry about any GATK tools that would allow you to annotate your output table, we do! 

    Funcotator is a functional annotation tool that allows users to add annotations to called variants based on a set of data sources, each with its own matching criteria. Please find the tool index for Funcotator here. There are a variety of Funcotator-specific arguments allowing you to customize your annotations within the index.

    I hope this helps! Please let me know if you find success with this tool. If you have any other questions as you go along, please don’t hesitate to reach back out.

    Best,
    Anthony

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    Anthony Dias-Ciarla

    Hi Leslie Youtsey,

    We haven’t heard from you in a while so we will be closing out your ticket in our system. If you still require assistance, you need only respond to this thread, and we’ll make you a follow-up ticket to pick up where we left off.

    Thank you again for contributing to our GATK forum!

    Best,
    Anthony

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