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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 using one sample split in two bam files

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    Anthony Dias-Ciarla

    Thank you for your post, elena vigorito ! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

    Please see our Support Policy for more details about how we prioritize responding to questions. 

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    Anthony Dias-Ciarla

    Hi elena vigorito,

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

    In this case, you can use the MergeSamFiles (Picard) tool. This tool will allow you to merge your BAM files from different read groups into a single file. You’ll want to combine these before inputting them into HaplotypeCaller. Please find an example command below.

    java -jar picard.jar MergeSamFiles \
         I=input_1.bam \
         I=input_2.bam \
         O=output_merged_files.bam

    I hope this helps! Please let me know if you find success with this. If you have any other questions, please do not hesitate to reach out.

    Best,
    Anthony

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    Anthony Dias-Ciarla

    Hi elena vigorito,

    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 create 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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