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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

read starts with deletion. Cigar: 4D150M

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    Bhanu Gandham

    HI iOOv

     

    This might be a bug and we are investigating it. You can follow the progress for this issue here: https://github.com/broadinstitute/gatk/issues/6490

     

    To help us troubleshoot and fix this bug can you please share with us following:

    1. From the BAM file please share the problematic read with read name: Read A00262:316:HLW5MDSXX:3:1346:7844:3646 CHR01:1602331-1602484
    2. Please share with us the the input BAM as well

    You can find instructions to share data here: https://gatk.zendesk.com/hc/en-us/articles/360035889671

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    deni

    Hi Bhanu Gandham!

    I'm having the same problem with more than one sample. I've also tried with FixMateCigar but the problem remains.

    "A USER ERROR has occurred: Read V300027291L3C003R0600645615 chr1:7026632-7026698 is malformed: read starts with deletion. Cigar: 3D64M36H. Although the SAM spec technically permits such reads, this is often indicative of malformed files.

    A USER ERROR has occurred: Read V300027291L1C002R0370459277 chr9:17352390-17352461 is malformed: read starts with deletion. Cigar: 2D70M30H. Although the SAM spec technically permits such reads, this is often indicative of malformed files.

    A USER ERROR has occurred: Read V300027195L4C005R0700962375 chr10:18036769-18036845 is malformed: read starts with deletion. Cigar: 20D57M43H. Although the SAM spec technically permits such reads, this is often indicative of malformed files.

    ..."

    Denise

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    iOOv

    I am sorry that I have removed these files as I have successfully done the analysis by gatk 4.0.4.0. But I remember that there are reads mapped with large hard or soft clip as SUPPLEMENTARY mapping near the regions the reads with error report  mapped. I hope  this may helpful.

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    David Benjamin

    iOOv deni A bug fix is currently in code review: https://github.com/broadinstitute/gatk/pull/6498

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