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  • bcftools for finding unique SNP

    Hi,

    Would appreciated some help, I am a neophyte when it comes to dealing with vcf files.

    I have 5 vcf files each represented a unique individual of the same species. I would like to filter the vcf's for snps that are unique to each individual thus ending with 5 vcf one for each individual contain snp not found in any of the other vcf files. Secondly I would like to setup a filter that removes SNPs that are with 36bases of each other.

    I have been using vcftools and bcftools to try and achieve the above for the unique part I have used bcftools isec -n -1 , is this correct ?

    Any help would be appreciated.

  • #2
    vcftools has a --thin option for removing SNPs that are too close.
    It also has a --max-maf for setting the maximum allowable minor-allele frequency. So setting that to 21% should give you SNPs that are in a single individual.

    After that, a custom script, or Excel :-( would extract the SNPs specific for each individual, or maybe use http://snpeff.sourceforge.net/SnpSift.html ? I'm not so familiar with it but it seems like it could do what you ask.
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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