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Maggie Sudo Pui San

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Latest activity by Maggie Sudo Pui San
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    Maggie Sudo Pui San commented,

    Hi Gökalp Çelik,   We do not have well-curated training resources for my species. Can I proceed with hard-filtering the merged VCFs? Is there anything I need to take note of when applying hard-filt...

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    Maggie Sudo Pui San commented,

    Hi Gökalp Çelik ,  Thanks for the advice. I have been following your suggestion to process the high and low-coverage samples separately. Now I am almost at the stage where I have to combine them. I...

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    Maggie Sudo Pui San commented,

    Hi there,  Thanks for the suggestion! I will look into the parameters as recommended and proceed from there.  Best,  Maggie. 

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    Maggie Sudo Pui San commented,

    Hi Gökalp Çelik  Thank you for the suggestion. My samples are very different in their coverage, some have up to 40X and some as low as 0.5X. In that case, does it make sense if I perform a few roun...

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    Maggie Sudo Pui San created a post,

    Updating GenomicsDB workspace with additional low coverage WGS

    Hi GATK team,  I would like to include additional samples with low genome coverage (0.5X to 2X) to my existing GenomicDB workspace. However, I have some doubts and hope to get clarification from th...

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    Maggie Sudo Pui San commented,

    Hi Bhanu,    Thank you! I'm relieved to hear that. I will check out the article for detailed documentation. Thanks. 

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    Maggie Sudo Pui San commented,

    I forgot to mention what I was trying to do in the previous post. I am performing variant calling for my whole genome sequences. The variants will be used to assess their phylogenetic relationship.

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    Maggie Sudo Pui San created a post,

    Recalibrated output (BQSR)

    Answered

    Hi, I have been using GATK version 4.2 for my work. The recalibration plot seemed to be acceptable ... However my cycle covariate plots looked a bit off. They have low log10 (observations) values o...

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    Maggie Sudo Pui San commented,

    Hi Bhanu Gandham    Okay I will do that

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    Maggie Sudo Pui San commented,

    Hello all, I have very similar output with John Denton's. However both my cycle covariate plots looked a bit off. They have low log10 (observations) values on the negative scale (-1 to -100++) of t...