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Szu-Ping, Chen

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Latest activity by Szu-Ping, Chen
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    Szu-Ping, Chen commented,

    1. Community
    2. Germline
    3. HaplotypecallerSpark error

    Hi Gökalp Çelik, We work on the inset genome data. However, most of the sequencing data don't have high integrity. Is it suitable to use the interval scattering method? Regards. 

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    Szu-Ping, Chen commented,

    1. Community
    2. Germline
    3. HaplotypecallerSpark error

    Hi again, I tried the method of adding the interval list to HaplotypeCallerSpark, and it had another similar issue at a different location. The part of the log file: Caused by: java.lang.IllegalArg...

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    Szu-Ping, Chen commented,

    1. Community
    2. Germline
    3. HaplotypecallerSpark error

    Hi Gökalp Çelik, Thank you for your reply.I've tried the Haplotyecaller for the same file. The whole file ran successfully and didn't have to have a bed file to pass the problematic region. The  ma...

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    Szu-Ping, Chen commented,

    1. Community
    2. Germline
    3. HaplotypecallerSpark error

    Hi Gökalp Çelik, Thank you for replying to the issue.I ran the  ValidateSamFile tool, and some errors about the NM tags were wrong. There is the log file: Running:    java -Dsamjdk.use_async_io_rea...

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    Szu-Ping, Chen created a post,

    HaplotypecallerSpark error

    1. Community
    2. Germline

    Hello, GATK team,   I'm using the HaplotypecallerSaprk to accelerate the variant calling step. However, I kept encountering the same problem, and I tried GATK 4.4.0.0 and GATK 4.1.8.0, and the resu...

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