Question: Extracting transcripts in gtf from reference with incorporation of variants from vcf
gravatar for drtamermansour
3.7 years ago by
United States
drtamermansour40 wrote:

I have my reference in a fasta format. My gene model generated by Cufflinks in a GTF format and genomic variants in VCF format. I want to extract the fasta sequences of  my transcripts from the reference but modified according to the VCF.

My thoughts

- if I changed the reference to a new consensus according to the VCF, the co-ordinates of GTF are ruined because of indels.

- if I got the transcripts from the reference first by gffread or getfasta, I can't use the VCF with the genomic co-ordinates to edit my transcripts.

- I tried to do liftover of the VCF from the genome to the transcriptome. I used UCSC kent tools (genePredToFakePsl then pslToChain) to make the chain file. Then I am using GATK to complete the liftover which fails (most probably because the FilterLiftedVariants can not manage the transcripts on the negative strand 

getfasta rna-seq vcf • 1.4k views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by drtamermansour40
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