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Add cnvkit gene level #47

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hsienchao opened this issue Jan 4, 2024 · 3 comments
Open

Add cnvkit gene level #47

hsienchao opened this issue Jan 4, 2024 · 3 comments
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enhancement New feature or request
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2024w03_0119

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@hsienchao hsienchao self-assigned this Jan 4, 2024
@hsienchao hsienchao added the enhancement New feature or request label Jan 4, 2024
@hsienchao hsienchao added this to the 2023w02_0113 milestone Jan 4, 2024
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Previously we intersected the cnvkit segment file with gene coordinates but the results might not be accurate if the gene is very short. Instead we should use command cnvkit.py genemetrics command to generate gene level log2 ratio from bin files.

To process the existing files on Frederick servers, I've Jiqui to install cnvkit for us. Now I processed one case (CHP212) and updated the web interface. I plan to run all samples next week.

@hsienchao hsienchao modified the milestones: 2023w02_0113, 2024w02_0112 Jan 4, 2024
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I have rerun 3500+ current cnvkit samples. Now I am uploading them to DB.

@hsienchao hsienchao modified the milestones: 2024w02_0112, 2024w03_0119 Jan 11, 2024
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Finished. I also generated the table of COG_UK and sent it to Xinyu.

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