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Alex Falconer

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Latest activity by Alex Falconer
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    Alex Falconer commented,

    1. Community
    2. Germline
    3. [Repost] ReadGroup missing when Applying BQSR

    ... and WSL is not recommended for production. Results may differ from real Linux (tested in WSL1).

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    Alex Falconer commented,

    1. Community
    2. Germline
    3. [Repost] ReadGroup missing when Applying BQSR

    Maybe someone will come in handy ... samtools reheader only changes the header. You needed to compare the results of the commands:samtools view -H Kuu_sorted_dedup.bam | grep '^@RG' samtools view K...

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    Alex Falconer commented,

    1. Tool Index
    2. 4.1.6.0
    3. ApplyBQSR

    gatk --java-options '-Xmx40G -Dsamjdk.compression_level=5' ApplyBQSR ...

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    Alex Falconer commented,

    1. Tool Index
    2. 4.0.11.0
    3. SamToFastq (Picard)

    # unavailable link https://gatkforums.broadinstitute.org/gatk/discussion/6484/how-to-generate-an-unmapped-bam-from-fastq-or-aligned-bam (A) Convert FASTQ to uBAM and add read group information usin...