Fasta Alternate Reference Maker extracted fasta files are same as reference

3

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9.3 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 • 3.3k views

ADD COMMENT • link updated 8.7 years ago by dsosa ▴ 10 • written 9.3 years ago by nuketbilgen ▴ 40

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

Thanks!

ADD REPLY • link 8.7 years ago by dsosa ▴ 10

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

ADD REPLY • link 9.3 years ago by Fabio Marroni ★ 3.0k

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Hi,

Sorry for my late response.

I have 3 genes in the vcf file.

Thank you

ADD REPLY • link updated 2.2 years ago by Ram 44k • written 9.3 years ago by nuketbilgen ▴ 40

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