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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

MergeBamAlignment conflicting headers between mapped and unmapped

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    Genevieve Brandt (she/her)

    Hi TA,

    We would expect that this tool should throw an error when the @RG tag information does not match. MergeBamAlignment is not the tool to fix this problem, other tools can fix this (such as the ones you mentioned).

    At the moment, does MergeBamAlignment throw an error as we would expect?

    Best,

    Genevieve

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    TA

    Hi Genevieve,

    Ok got it.

    Currently it is not throwing an error. It seems to resolve the conflict by using the @RG tag information from the unaligned BAM. This created an issue for me later on as during alignment I added RG tags to each mapping in the BAM. There was then a discrepancy between the RG tag in the header and the read group information for each mapping. This then created an error when I tried to do something else with this BAM with GATK because of this discrepency

    I have resolved the issue (I made sure to have the same @RGID in both unaligned and aligned BAM) but wanted to bring up this issue as other users might encounter. I agree it should give an error when you try to align an unaligned and aligned BAM with different RGIDs.

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    Genevieve Brandt (she/her)

    TA thank you for the response. I have created a ticket so that this tool will throw an error for this issue in the future: https://github.com/broadinstitute/picard/issues/1789

    Could you submit a small snippet of your files to recreate this behavior for testing purposes? Here are the instructions: https://gatk.broadinstitute.org/hc/en-us/articles/360035889671

    Thank you!

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