Is there any tool that could select variants from .BAM and make a .fasta file?

GenIvanGenIvan SpainMember

Hi all! I'm new in these kind of analysis. I need to select several specific regions from a .BAM file and make a .fasta one to do a data base in the future. Is there any tool that could help me?

Thanks Community,

Ivan

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Not directly from the bam, but if you call variants from your bam file to generate a vcf callset, then you can use the vcf to make a "mutant" fasta. See the reference utilities in the Tool Documentation.
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