I am studying allele specific expression and I am stuck on the step to get 2 transcripts (one from haplotype 1 and one from haplotype 2).
To get genes/transcripts from a GTF I use
cufflink gffreads: this is not a problem.
Now I want to make version 2 (ie. haplotype 2, or alternative) of these transcripts (from a .vcf I have): if these are SNPs, there are no issues but if I got indels then the coordinates of the GTF are not relevant anymore.
Someone have an idea how can I create the haplotype 2 transcripts?
Thanks a lot.