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JAY SINGH

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Latest activity by JAY SINGH
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    JAY SINGH commented,

    1. Community
    2. Other
    3. Error in running SplitNCigarReads - htsjdk.samtools.util.RuntimeIOException

    Hello Genevieve, I am using GATK 4.2.5.0. I am getting the same issue. Unfortunately, my issue is not solved after specifying --tmp-dir. Any other suggestion? Thanks and regards, Jay

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    JAY SINGH created a post,

    MarkDuplicates

    1. Community
    2. Other

    I have sorted my bam file by query name. what should be the --ASSUME_SORTED option in MarkDuplicates. In manual it is written about coordinate sorted bam file but not about query name sorted bam fi...

    • JAY SINGH
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    JAY SINGH commented,

    1. Tool Index
    2. 4.0.1.1
    3. MarkDuplicates (Picard)

    What should be the "--ASSUME_SORTED" option if the bam file is sorted by query name?