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

Exception in thread "main" java.lang.IllegalArgumentException: Alignments added out of order in SAMFileWriterImpl.addAlignment


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    Gökalp Çelik

    Hi Chloe Liu

    Can you post the header of your original input file? Also can you try running this using the latest GATK or Picard 3.10?


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