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  • How to extract SNPs between samples, but not between samples and reference.

    Hello,

    I have used samtools mpileup, and bcftools call/filter (v1.5) to call SNPs between 4 samples and a de novo reference transcriptome.

    I'm interested in extracting SNPs that occur between individual samples, and not between the samples and the reference. I would like to see how different each sample is different, or similar, from one another. Is this possible? I haven't been able to find much documentation on how one would approach this.

    Any info would be greatly appreciated.

    Cheers.

  • #2
    cross posted https://www.biostars.org/p/261007/

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