Bhanu Gandham
Computational Scientist
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Activity overview
Latest activity by Bhanu Gandham-
Bhanu Gandham commented,
Hi Maggie, These values look normal to me. Take a look at this article for detailed documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360035890531-Base-Quality-Score-Recalibration-B...
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Bhanu Gandham commented,
Hi Victoria Buswell For pooled samples our recommendation is to use Mutect2. Can you try to use Mutect2 instead of HaplotypeCaller for your variant calling and let me know if that works better?
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Bhanu Gandham commented,
Hi Maggie Sudo Pui San Can you please start a new thread with your question. Please post the exact commands you are using and the versions of tools you are using. Can you also pease give an expla...
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Bhanu Gandham commented,
Hi , I am going to move your post into our Community Discussions -> General Discussion topic, as this topic is for reporting bugs and issues with GATK. You can read more about our forum guidelines ...
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Bhanu Gandham commented,
Hi , I am going to move your post into our Community Discussions -> General Discussion topic, as the Special GATK Use Cases topic is for reporting bugs and issues with GATK. You can read more about...
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Bhanu Gandham commented,
Hi Chloé Girard I think you might have missed that last step of sending us the files. The instructions on how to send us the files are provided in the article mentioned above.
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Bhanu Gandham commented,
Hi Chloé Girard Can you please share with me the reference you are using and the vcf file? I would like to recreate this error on my end to figure out why this is happening. Please follow instruc...
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Bhanu Gandham commented,
Hi , I am going to move your post into our Community Discussions -> General Discussion topic, as the Germline topic is for reporting bugs and issues with the GATK tools. You can read more about o...
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Bhanu Gandham commented,
Hi , I am going to move your post into our Community Discussions -> General Discussion topic, as the Germline topic is for reporting bugs and issues with GATK. You can read more about our forum gui...
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Bhanu Gandham commented,
Hi Chloé Girard Hi For what you are trying to do use VariantFiltration over SelectVariants. Also there are some other corrections to made in the command you are using: --filter-expression is used...