How can we convert a vcf to fasta, so that I can blast some genes against that whole genome sequences?

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5 months ago

Harshita • 0

I want to use my whole genome sequence which is in vcf format to .fa, so that I can find some genes using BLAST.

blast fasta vcf gene • 411 views

ADD COMMENT • link updated 5 months ago by Ram 44k • written 5 months ago by Harshita • 0

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You cannot convert a VCF to a FASTA as they have vastly different information content. Please explain your process - what exactly do you want to "convert"?

ADD REPLY • link 5 months ago by Ram 44k

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well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker but as your VCF was called from a reference genome do you think you'll find something new for a few variants ?

ADD REPLY • link 5 months ago by Pierre Lindenbaum 164k

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