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

MarkDuplicatesSpark error: Detected multiple mark duplicate records objects corr esponding to read with name

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    Bhanu Gandham

    Hi Jejust

     

    Since Longranger is not part of our best practices, we are unable to help you out with this issue. We don't have much experience with that aligner.  This might be a question for  SeqanswersBiostars, or Bioinformatics Stack Exchange

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    Jejust

    Thank you for your quick answer, Bhanu.

     

    For the records, I discovered that MarkDuplicates from Picard works perfectly on the output of LongRanger (just apply SortSam, even if it's supposed to be already sorted by coordinate), and even has options to use the barcodes (BARCODE_TAG, READ_ONE_BARCODE_TAG, etc).

     

    Thanks for your work!

    Jérémy.

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