Bhanu Gandham
Computational Scientist
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Activity overview
Latest activity by Bhanu Gandham-
Bhanu Gandham commented,
Hi Jan, I apologize for the delay in getting back to you. I was attending a conference. Can you please try the latest version of GATK which is v4.2.2.0. The version you are using is quite old at th...
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Bhanu Gandham commented,
Hi Mingzhou Fu, 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 ou...
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Bhanu Gandham commented,
Hi Diya, Please post the exact command you are using, the version of the tool and the entire error log.
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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 with GATK. You can read more about our forum guidelines and the top...
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Bhanu Gandham commented,
HI, Unfortunately, we do not support GATK3 anymore. Please upgrade to the latest version of GATK4. Thank you!
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Bhanu Gandham commented,
Hi , I am going to move your post into our Community Discussions -> General Discussion topic, as the non-human topic is for reporting bugs and issues with GATK. You can read more about our forum gu...
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Bhanu Gandham commented,
Hi , Thank you for your post. We are currently prioritizing bugs and errors with GATK tools. You can read more about our forum guidelines and the topics here: Forum Guidelines. We are tracking do...
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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...