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bcftools view to find a base at a certain position for a set of samples

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  • bcftools view to find a base at a certain position for a set of samples

    I have a humongous vcf.gz file with a bunch of whole genome sequences of dogs. I want to find a base at a specific position for a select number of those samples. I think that I should use -t/-T to find the position and -s/-S to specify which samples to check but I am not sure. I also don't know what the command should look like. If someone could give an example of what the command should resemble, that would help me a ton.

    I checked a couple other threads on here but they don't seem to be exactly what I need, or if they do I don't quite understand correctly. (In which case, could someone please explain)

    Thank you!

  • #2
    Answered here: http://seqanswers.com/forums/showpos...24&postcount=8

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