Question: Fasta Alternate Reference Maker extracted fasta files are same as reference
gravatar for nuketbilgen
4.1 years ago by
United Kingdom
nuketbilgen30 wrote:


I need to extract fasta sequences for two genes. I used 

java -jar /Users/nuketbilgen/programs/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R $REF -o YK20.fasta -L bTau7_2and6_subset.bed -V YK20_S24S12.raw.g.vcf

but it does not seem to work all of the output fasta files have the same sequence as the reference. Is it because of the raw vcf file? 

ADD COMMENTlink modified 3.5 years ago by dsosa0 • written 4.1 years ago by nuketbilgen30

Do you have SNPs in the two genes in the vcf file you fed to GATK?

ADD REPLYlink written 4.1 years ago by Fabio Marroni2.3k


Sorry for my late response.

I have 3 genes in the vcf file. 

Thank you.

ADD REPLYlink written 4.0 years ago by nuketbilgen30
gravatar for dsosa
3.5 years ago by
dsosa0 wrote:

I was wondering you were able to figure out this issue? I'm having the same problem.


ADD COMMENTlink written 3.5 years ago by dsosa0
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