Fasta Alternate Reference Maker extracted fasta files are same as reference

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

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updated 10.4 years ago by dsosa •

• written 11.0 years ago by nuketbilgen •

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

• 0 views • link

written 11.0 years ago by Fabio Marroni

Hi,

Sorry for my late response.

I have 3 genes in the vcf file.

Thank you

• 0 views • link

updated 3.9 years ago by Ram

• written 10.9 years ago by nuketbilgen •

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

Thanks!

• 0 views • link

written 10.4 years ago by dsosa •

0 answers

No answers yet.

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