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Khalil Jahed

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Latest activity by Khalil Jahed
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    Khalil Jahed commented,

    Hi Genevieve-Brandt-she-her, Comparing the quality score accuracy of before and after ApplyBQSR, the accuracy has been improved afterward where the mean quality score decreased - which I think is c...

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    Khalil Jahed created a post,

    ApplyBQSR reduces reads quality

    ApplyBQSR reduced reads quality from 70 to 50 (in ASCII scale). The known-sites used in this step, were first generated from the same sample without ApplyBQSR. These variants were limited to only h...

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    Khalil Jahed commented,

    Similar question I have. How can one find these known sites for non-model organisms eg. crops? 

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    Khalil Jahed created a post,

    Variant Filtration - FS and SOR are not supported

    Answered

    Hi, The FS and SOR variant filtration options do not work. Are they still active? NOTE: AB and MQ work using the same command. GATK/4.14.1 was used.  Command lines:  gatk VariantFiltration \ -R ref...

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    Khalil Jahed commented,

    Hi Sushma, I got updated!  

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    Khalil Jahed created a post,

    Where to find old discussion

    Hi, It seems that the old discussion on this forum is not accessible. Can we still retrieve those posts and comments?