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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

LeftAlignIndels issue - process done in 5 seconds and output file is only 3kb

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    Genevieve Brandt (she/her)

    Hi Jonas Andersson,

    Could you validate your input BAM to see if there are problems there?

    • Validate your Sam or Bam file with ValidateSam following this tutorial.
    • Please also provide details about how you obtained your data.

    It also looks like 441079 reads were filtered by the WellformedReadFilter, how many reads did you start with?

     

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    Jonas Andersson

    Thanks for helping me solve this! Validation showed ERROR:MISSING_READ_GROUP. 

    I solved it by adding the groups with bwa mem -R options.

     

    But I have to talk to my supervisor why this happened.

    The data was obtained by Illumina sequencing. It resulted in 4 library files of ~40 Gb each. I took a fragment from one of the files to be able to test my python script without being so time consuming. Maybe it was because of that? Do you know why? Because it worked when my supervisor ran the large files earlier this year.

     

    Best / jonas

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    Genevieve Brandt (she/her)

    Jonas Andersson glad that you were able to figure out a solution! I cannot be sure why you had an issue with read groups and your supervisor did not. Read groups are necessary for running GATK. You would need to compare all steps of the pipeline you both ran and the commands to determine why it worked and you needed to add read groups.

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