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Old 09-25-2015, 03:12 AM   #1
Junior Member
Location: Cali

Join Date: Sep 2015
Posts: 4
Default I Have Variants and positions and need to make a GTF file. Help

I'm very new to this and I'm working on my first project. I have a list of Variants and their location. I have been tasked with creating a GTF file of this data and then seeing where the data points land. I have searched and have a wealth of knowledge on what makes up the GTF file, why its used, blah blah. But I Still have no idea how to convert the limited amount of data (3 columns) of data that i have into the larger file format of GTF. Please advise. It'd be MUCH appreciated!

The goal of this piece of the project is to use the coordinates of Variants to find their location in the annotation and then visualize it.

Last edited by JdevSEQnoob; 09-25-2015 at 03:34 AM.
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Old 09-25-2015, 09:29 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Just skip making a GTF and use the VCF file that you presumably already have. You can directly use a VCF file with IGV for visualization or things like bedtools for whatever sorts of intersects you might find useful. It's quite likely that many of the tools that you want to use already support the format you have.
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annotation, expression analysis, gtf

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