Samuel Quaynor
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Activity overview
Latest activity by Samuel Quaynor-
Samuel Quaynor commented,
Hello Gökalp Çelik,Are there standard quality thresholds for QA and QS for the segmented CNV calls? I want to filter the calls based on the qualities but I am yet to find what the threshold qualiti...
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Samuel Quaynor commented,
Thank you so much Gökalp Çelik, I have been able to do that and successfully call the copy numbers.Grateful for all the help A snapshot of part of the segmental call:
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Samuel Quaynor commented,
Gökalp Çelik, thanks for the yaml file. I have created the environment with the yaml file and run a pip on the pyhtonpackage.zp. How do I install gatk now since it is not part of the packages in th...
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Samuel Quaynor commented,
Gökalp Çelik, if I create the new environment with the gatkcondaenv.yml, does it mean I'd have to rerun the commands from the beginning (i.e PreprocessIntervals) or I can continue from where the er...
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Samuel Quaynor commented,
please can you provide me the link to the yml file?
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Samuel Quaynor commented,
I created a conda environment and downloaded GATK version 4.3.0.0 and python3.6.10. I then downloaded gcnvkernel and all it's dependencies. I have been running the commands in this environment.Init...
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Samuel Quaynor commented,
Thank you Gökalp Çelik. I have been able to figure out what the problem was. I made a mistake in the name of the directory. I typed temp_0001_of20/scattered.interval_list instead oftemp_0001_of_20...
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Samuel Quaynor commented,
Hello Gökalp Çelik, below is the command I used in creating the scatter gatk IntervalListTools \ --INPUT filtered_intervals.interval_list \ --SUBDIVISION_MODE INTERVAL_COUNT \ --SCATTER_CONTENT 10...
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Samuel Quaynor commented,
I wanted to also know if I could just run the GermlineCNV without creating the scatters?
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Samuel Quaynor commented,
Thank you for the clarity Gökalp Çelik. I run the below command for my samples but I ended up with an error gatk GermlineCNVCaller \ --run-mode COHORT \ -L cnv/gatk_cnv/scatter/temp_0001_of20/s...