Question: vcf to fasta
gravatar for ajmaninisha
3.4 years ago by
ajmaninisha30 wrote:



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



mpileup-vcf-fasta = new reference annotation

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





ADD COMMENTlink modified 3.4 years ago by Jennifer Hillman Jackson25k • written 3.4 years ago by ajmaninisha30
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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:


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. 

Paste, Cut, Merge Columns

There are other options. A search over at 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 COMMENTlink written 3.4 years ago by Jennifer Hillman Jackson25k
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