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knausb / vcfR

Tools to work with variant call format files
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gene/chromosome annotation #202

Closed umasstr closed 2 years ago

umasstr commented 2 years ago

Hi Brian, thank you for releasing a really well-made package.

I am having trouble understanding what the GFF is used for. From the tutorial, it doesn't look like there's a way to annotate gene names/position on heatmaps, qc plots etc. Ideally, I would like to annotate genes at which there is an SNV found.

Somewhat related, I was hoping to make end-to-end chromosome plots. I'm dealing with several samples (25) and It would be great not to have to plot the chromosomes one-by-one.

Any advice you could provide would be much appreciated!

knausb commented 2 years ago

Hi @umasstr ,

The GFF is used to plot annotations in the chrom plot. I don't think it'll help you making annotation though.

In order to make end-to-end chromosomes you could try the following.

?vcfR::rePOS()

Good luck! Brian

umasstr commented 2 years ago

Thanks!