VIsualization of VAriants: A VCF File Visualization Tool

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3.7 years ago

yousefifariba6 • 0

Hi, I got the VCF file from the software VARSCAN2 and I want to display it statistically as a graph or a visible plot. What steps should I go through? My file contains 1534 variant positions reported and I realized I had to do the filter first. Am I guessing right? Please share the steps for plot display.

RNA-Seq • 2.5k views

ADD COMMENT • link 3.7 years ago by yousefifariba6 • 0

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What exactly do you wish to plot? Can you describe what your X and Y axis scales (and your legends) would look like?

ADD REPLY • link 3.7 years ago by Ram 43k

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Linked thread: julia viva for loking vcf file

ADD REPLY • link 3.7 years ago by Kevin Blighe 87k

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That piece of software has no sample visualizations, which is unusual for visualization packages. OP - maybe take a look at this: https://github.com/knausb/vcfR

ADD REPLY • link 3.7 years ago by Ram 43k

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Should the first vcf file be filtered and then extracted?

ADD REPLY • link 3.7 years ago by yousefifariba6 • 0

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Are there multiple VCF files? What are you looking to filter or extract?

ADD REPLY • link 3.7 years ago by Ram 43k

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