Genome Analysis Toolkit

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

GenomeSTRiP SVPreprocess failed

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    Genevieve Brandt (she/her)

    Thank you for your post Jenny Xu. I'm going to tag Bob Handsaker to get back to you shortly.

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    Bob Handsaker

    This is most likely because your input bam/cram files do not contain library information (i.e. there is no LB tag on the @RG headers). It is strongly recommended that you inject library information, since the technical characteristics of the data (insert size distribution, GC-bias, etc.) depend on the library.

    If your headers are missing the LB tag, there are three choices. First, you could reheader your input files to make them compliant.

    Second, you could use `-libraryKey READGROUP`. This will cause each read group to be treated like a separate library.

    Third, you could try an experimental undocumented feature that allows you to remap read group information on the fly. To do this, you must first pre-create your metadata directory and inside the directory create a text file read_groups.dat. This should be a tab delimited text file with three columns with headers READGROUP SAMPLE LIBRARY. This will override the information from the headers in the input file (specifically SM and LB), based on the read group IDs. To use this, all of your read group IDs must be unique across all input files.

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    Jenny Xu

    Thanks Bob. Adding the LB tag in the header solves the issue. 

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