wiki97
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Latest activity by wiki97-
wiki97 created a post,
Somatic Structure Variation on exome-seq data
category of my question: a)How do I (......)? Hi, I am new to GATK exome-seq and would be grateful for any suggestions :) I am planning to use GATK4 to perform Structure Variation analysis on whole...
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wiki97 commented,
Ok, thank you very much for your help!!
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wiki97 commented,
Dear David Benjamin, thank you very much for your help!
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wiki97 commented,
Dear David Benjamin, thank you very much for your answer! Do I understand correctly that FilterMutectCalls already takes into account the number of reads at the given position and the number of rea...
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wiki97 commented,
I run ValidateSamFile and got "No errors found" message, the ValidateVariants gave "Processed 89324 total variants in 8.6 minutes" message and no error/warning information. Here are first few lin...
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wiki97 commented,
No, there were no warnings/errors.. I received the "SUCCESS" message from MuTect2.
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wiki97 commented,
Dear David Benjamin, thank you very much for your answer! After MuTect2 I ended up with 90,000 variant calls. Then I used FilterMutectCalls and took calls with "PASS" in the FILTER column (created ...
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wiki97 commented,
Dear Genevieve Brandt, thank you very much for your answer. Yes, I do have AD values but I have just realized what the problem is - in the QUAL column I cannot find any values, there are dots in al...
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wiki97 created a post,
MuTect2 annotations
AnsweredCategory for my question: "d) Where do I find (......)?" Hi, I am new to exome-seq and would be grateful for any suggestions :) I want to check coverage for variants called with MuTect2 (GATK 4....
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wiki97 commented,
Dear Genevieve Brandt, thank you very much for your answer! I have already read this article, however I am not sure what is the reason for the lack of this specific annotation.. Is QualByDepth spec...