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  • Extract flanking sequence of SNP call

    Hi all.

    I have mapped sequencing data to a reference using BWA and called SNP using samtools mpileup and generated a vcf using bcftools. What I would like to achieve is to extract the SNP along with a 35base flanking sequences. I would appreciate any help with this.

    Thanks

  • #2
    bedtools always comes to mind when asking questions like "how to extract sequence". It should be easy to convert the VCF single coordinate into the start & end coordinates for a BED file (Excel or other spreadsheet program or a simple Perl/Python script). Then use fastaFromBed.

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    • #3
      samtools faidx, when given genomic coordinates, will make a fasta of the desired region. That another way, using software you've already got.

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