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John Denton

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Latest activity by John Denton
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    John Denton commented,

    Okay. I will post the outcome of the reanalysis (yea or nay) when it is available.

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    John Denton commented,

    Thanks! I have seen the BETA doc. Are there any performance comparison docs (in terms of calls, base quality scores, coverages, etc) available for Spark vs traditional? I am wondering what the mean...

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    John Denton commented,

    Hi Genevieve, Great! I just restarted it. It is unclear based on the several forum posts I have seen since late 2018. Is HaplotypeCallerSpark okay to use for production? I have seen the following: ...

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    John Denton created a post,

    haplotypecallerspark wants DS_Store

    I tried running HaplotypeCallerSpark using the following command: gatk --java-options "-Xmx32g -XX:ParallelGCThreads=1" HaplotypeCallerSpark --spark-master local[$NTHREADS] --reference $REF --input...

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    John Denton commented,

    Thanks for the clarification on this! A colleague of mine and I were wondering about those uncalibrated scores. So the post-BQSR outputs appear to be okay to use, and the cause of the pre-calibrati...

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    John Denton created a post,

    bqsr output issue

    I have bqsr plots that do not seem to make sense, and I am wondering what troubleshooting can be done. I'm using gatk 4.1.4.1 to generate variants for a project on a non-model organism. I'm at the ...

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    John Denton created a post,

    read groups for samples on one flow cell + 1 lane

    I am using GATK 4.1.4.1, and am analyzing 4 samples of one non-model species (Illumina data), sequenced on the same flowcell, in the same lane. The files I have were provided demultiplexed, and the...