Question: Fasta Alternate Reference Maker extracted fasta files are same as reference
2
gravatar for nuketbilgen
23 months ago by
nuketbilgen30
United Kingdom
nuketbilgen30 wrote:

Hi!

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 16 months ago by dsosa0 • written 23 months ago by nuketbilgen30

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

ADD REPLYlink written 23 months ago by Fabio Marroni1.3k

Hi, 

Sorry for my late response.

I have 3 genes in the vcf file. 

Thank you.

ADD REPLYlink written 23 months ago by nuketbilgen30
0
gravatar for dsosa
16 months ago by
dsosa0
dsosa0 wrote:

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

Thanks!

ADD COMMENTlink written 16 months ago by dsosa0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1167 users visited in the last hour