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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

DepthOfCoverage (BETA) Follow

4 comments

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    Brian Wiley

    When I run this tool with command below, I just get the refseq file printed to stdout and the files are blank.

    gatk DepthOfCoverage -R $HG19 -I bams/bamRG/SRR10022835.md.bam -L intervals.bed -gene-list chr17_genes.gtf -O depth.SRR10022835

    I got the refseq gene list in GTF format from the table browser.  Is this wrong format?  The program runs.

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    Brian Wiley

    Ok I see I am getting error:

    14:33:56.869 ERROR AbstractGtfCodec - Gene Feature Aggregation: Exon store not empty: [chr17

    ...

    at org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec.decode(AbstractGtfCodec.java:230).

    I think we need better documentation at https://gatk.broadinstitute.org/hc/en-us/articles/360035532032-RefSeq-gene-list-format.  I basically need to guess what format to use (BED?, GTF?, all fields?) for the refGene table.

    EDIT

    I found the format now (https://github.com/broadinstitute/gatk-docs/blob/master/gatk3-methods-and-algorithms/Performing_sequence_coverage_analysis.md) and I have it correct and am getting:

    A USER ERROR has occurred: Cannot read file:///export/home/bwiley4/data/project/rest/list.txt because no suitable codecs found

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    Brian Wiley

    I got it to work by making sure the name of file ended with ".refseq" with a lower case "s" in "refseq".  We really need to make sure this is included here https://gatk.broadinstitute.org/hc/en-us/articles/360035532032-RefSeq-gene-list-format.  This is an easy thing to document :)

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    Wei

    -ct or --summary_coverage_threshold are not working in GATK4.1.8?  

    It gave
    **BETA FEATURE - WORK IN PROGRESS**

    USAGE: DepthOfCoverage [arguments]

    Generate coverage summary information for reads data
    Version:4.1.8.1

    then available usage info not including above two options. Thanks!

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