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Calum Tattersfield

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Latest activity by Calum Tattersfield
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    Calum Tattersfield commented,

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    3. My recalibration table from BaseRecalibrator is empty

    So it looks like I have 8000000 reads in the marked duplicates bam file as well. # Read countsamtools view -c 102_002_002_test_001_markedDupes.bam8000000# First 3 rowssamtools view 102_002_002_test...

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    Calum Tattersfield commented,

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    3. My recalibration table from BaseRecalibrator is empty

    Thanks for your reply Genevieve! Here is what I'm seeing for after BaseRecalibrator but the table is empty (as shown), and then when I go to ApplyBQSR I get the read group error. Recalibrating base...

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    Calum Tattersfield created a post,

    My recalibration table from BaseRecalibrator is empty

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    GATK version 4.1.9 c) Why do I see (......)? Nothing in my recalibration table I have been following this pipeline. But my baserecalibrator does not seem to be working. See below. My function call...

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