Modifying genome GTF file based on vcf information
Hello, I'm trying to generate new reference annatoation file(GTF) of sub-population (or ecotype). Currently, I have reference genome annotation file(GTF) and vcf file from the sub-population. but I am now afraid using current reference genome annotation file(GTF) becuse indels would ruine the orignal coordinates of GTF.
So Is there any tools for shift orginal GTF coordinate base on VCF ?
Thank you very much!
• 1,933 views
•
link
written
by
jihwan8611 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Generate Read counts from bam file
written by singhankit973 •
-
What is the output of rna-seq alignment to reference transcriptome (FASTA+GTF) look like in SAM for…
written by sonsunjirachote •
-
Annotating variants using latest version fof the genome
written by prasundutta87
-
Recreating the gtf file for new reference
written by fritzforbang160 •
-
Ask for a tools which can mirror the result of FastaAlternateReferenceMaker to an annotation file
written by ysas •
-
Haplotype phasing for non-human model organism
written by kirannbishwa01
-
Extracting transcripts in gtf from reference with incorporation of variants from vcf
written by drtamermansour •
-
Modifying fasta file based on vcf information
written by Jautis
-
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, …
written by Malachi Griffith
-
How To Get Snps Matrix For Population Genetic Ananlysis From Snps Variant Files
written by Jianfengmao •
I have the same problem:) Did you find a solution?