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Tools to create flanking sequences for variants based on a VCF file and reference genome.

Are there publicly available tools that can create flanking sequences for a set of variants + sample names based on a VCF file and a reference genome?

I am looking for such a tool that also takes the flanking variants/genotypes in to account of the specified samples. If there are flanking alternative genotypes for the specified samples the nucleotide at that position in the flank should be changed to a IUPAC.

This seems like a to common thing to write something myself.

Something like vcfprimers in vcflib but then with the additional functionality

  1. to specify just a few variant by ID or positions
  2. that flanking variants/genotypes of a specified set of samples can be used to put IUPACS in the flanks (the IUPACS cover the reference allele and the alleles of the specified samples at that location)
  3. handle flanking indels, by either using them in the flanking sequence or giving a warning for these variants

https://github.com/vcflib/vcflib#vcfprimers

vcf assay
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updated by estpallag • estpallag • written by William William

1 answer

Hi William,

I need exactly the same. Did you figure it out?

Thanks,

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written by estpallag • estpallag

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