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Thandeka

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Latest activity by Thandeka
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    Thandeka commented,

    @Bob thank you let me download it again and run the script

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    Thandeka commented,

    I don't think I quite understand what you mean. I used the above commands and this was the output: $ ls -l Homo_sapiens_assembly38.lcmask.fasta-r--r--r-- 1 marhwayiza cbio-group 793259520 Jul 10 16...

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    Thandeka created a post,

    Genome STRiP CNV Discovery pipeline error

    If you are seeing an error, please provide(REQUIRED) : a) Genome STRiP version used: 2.00.1958b) Exact command used: #run cnv discoveryjava -cp ${classpath} ${mx} \org.broadinstitute.gatk.queue.QCo...

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    Thandeka commented,

    Bob Handsaker thank you very much, I think using the sample_gender.report.txt produced by preprocessing is the best option  

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    Thandeka commented,

    I did not have any specific reason, I think the best way would be to use the sample_gender.report.txt because I thought its a requirement to have a gender map file. It does not have a header, its a...

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    Thandeka commented,

    The issue is with the highlighted sample (ERR1955423). I have attached an image of the gender map file. and also posted a part of the file. I'm doing an analysis of over 200 samples.  190618_FD0925...

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    Thandeka created a post,

    GenomeSTRiP analysis error

    If you are seeing an error, please provide(REQUIRED) : a) GenomeSTRiP version 2.00.1958 ##### ERROR stack trace org.broadinstitute.sv.commandline.ArgumentException: Unrecognized gender for sample E...

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    Thandeka commented,

    Bob Handsaker thank you for the response, this has really helped me. 

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    Thandeka created a post,

    GenomeSTRiP analysis

    If not an error, choose a category for your question(REQUIRED):a) Will using GenomeSTRiP to analyze different datasets in terms of coverage, read-base pairs, PCR vs PCR-free, affect the results I w...

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    Thandeka commented,

    Hi Bob the, -jobWrapper argument worked I am no longer getting errors, but the only problem I have now is that in the output directory there is nothing and when I open the log directory and read it...