Genevieve Brandt
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Activity overview
Latest activity by Genevieve Brandt-
Genevieve Brandt commented,
We don't have anything like that, which is why it is in BETA. Sorry for no better news! There may have been discussions in the past available on this forum or our old forum where other users discus...
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Genevieve Brandt commented,
You may want to verify that R is working correctly, please see again the Tools Involved section in the tutorial. If you are having issues, try using GATK in a docker container.
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Genevieve Brandt commented,
HaplotypeCallerSpark is still BETA, which for this tool means we do not recommend it for production pipelines and we cannot guarantee the results are the same as the normal HaplotypeCaller. However...
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Genevieve Brandt commented,
Hi John Denton, My team was able to take a look and thinks it may be a transient error that could go away. Would you be able to re-run this command and see if you get the same issue? HaplotypeCalle...
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Genevieve Brandt commented,
Hi Yuanyuan Wu, I brought this up with our developer team to confirm it is not a bug and I think we have found the issue! The input for DenoiseReadCounts should be a file downloaded from the tutori...
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Genevieve Brandt commented,
Our best available information is in our best practices, where we go over the steps we recommend and the purpose. If you are doing germline short variant discovery, you can find the information here.
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Genevieve Brandt commented,
Hi Yuanyuan Wu, The error message is reporting that you do not have a non-negative sample median (it is mostly likely zero) which is in your tumor.counts.hdf5 file. You can examine the count file t...
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Genevieve Brandt commented,
I think there is something important to clarify - the goal of BQSR is not to filter out reads, it changes the quality scores in the reads to correct systematic bias from the sequencer. If you haven...
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Genevieve Brandt commented,
Hi vivekruhela, Thank you for joining in on the discussion on github to help us find the issue quickly! When doing the liftovers you will want to make sure that all the naming conventions are consi...
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Genevieve Brandt commented,
Hello vivekruhela, Thanks for reposting! I have created a ticket on our github repository because I was not able to get to the bottom of this issue. You can see it here and follow along with what t...