Question: Tools to create flanking sequences for variants based on a VCF file and reference genome.
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gravatar for William
2.4 years ago by
William4.3k
Europe
William4.3k wrote:

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

assay vcf • 1.0k views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by William4.3k

something like Construct a combination set of fasta sequences from a vcf ?

ADD REPLYlink written 2.4 years ago by Pierre Lindenbaum115k
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