Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: vcf to fasta
0
gravatar for ajmaninisha
3.4 years ago by
ajmaninisha • 30
Canada
ajmaninisha • 30 wrote:

Hi,

 

i want to generate fasta files of my mapped sequence rather than the reference genome:

so i am following this workflow , please correct me :

mpile up on bam datasets (output format vcf) and now i want to convert this vcf into fasta 

Ques 1. Is there any tool which will directly convert vcf to fasta and is it available on galaxy toolshed or main.Have heard about FastaAlternateReferenceMaker

 

workflow:

mpileup-vcf-fasta = new reference annotation

gffread- assembled transcript + new reference annotation = fasta of my sample 

 

Thanks

 

Nisha
fasta alternate reference maker galaxy • 3.6k views
ADD COMMENT • link •
modified 3.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.4 years ago by ajmaninisha • 30
1
gravatar for Jennifer Hillman Jackson
3.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

When using Main, please see the tool is in the group "NGS: VCF Manipulation" and "FASTA Manipulation".

For just the content in the VCF file, run these two:

VCFtoTab-delimited
Tabular-to-FASTA

If you want attach (genomic) flanking sequence, these tools can be used with the others in combination to obtain longer sequence with the alternate allele swapped in. 

VCFprimers
Paste, Cut, Merge Columns

There are other options. A search over at https://www.biostars.org will provide a spectrum of methods people use. If a tools hasn't been wrapped for Galaxy yet, and you want to do that, it would be welcomed in the Tool Shed. If our team has more updates, will post back here.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour