Fasta Alternate Reference Maker extracted fasta files are same as reference
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7.3 years ago
nuketbilgen ▴ 40

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?

FastaAlternateReferenceMaker GATK • 2.8k views
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I was wondering you were able to figure out this issue? I'm having the same problem.

Thanks!

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

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Hi,

Sorry for my late response.

I have 3 genes in the vcf file.

Thank you

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