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3.9 years ago
fritzforbang160
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0
Hello everyone, I used the GATK FastaAlternateReferneceMaker to create an alternate reference genome from a reference FASTA and a VCF file. My new alternate reference is longer than the original reference and I assume it is because of the indels. My question is how can I update the gtf file of the original reference to produce a gtf file for the alternate reference. Any help will be appreciated. Thanks
What is the purpose of this exercise? The location of transcripts on a reference genome build won't change just because you have a custom genome sequence.