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Comparing and combining vcf files

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  • Comparing and combining vcf files

    Hi,

    I am trying to determine if there is an available solution for comparing vcf files and combining them into a single, non-redundant file?

    So for example, if I have two vcf files for two patients, I would like to create one unique list of all the mutated locations observed in their genomes. Is there anything else out there or should I just script something?

    Thanks in advance.

  • #2
    you can use samtools mpileup to compare 2 vcf files at the same time.

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    • #3
      So you want the union of both files? Try vcftools or BEDTools.

      I don't think that mpileup will work with vcf files. What it will allow you to do is to take multiple .bams at once, and make one multi-vcf. But if you don't have the .bams, that won't help much.

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      • #4
        BEDTools appears to be what I am after - cheers!

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