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  • vcf-merge

    Hi

    I have several vcf files, raw and annotated.
    I've used vcf-merge without any option. The output file I used it check for recurrent mutations.

    I'm not able to understand (as the documentation is almost none). When vcf-merge merges vcf files is it doing it by position?

    What happens if I have something like (being each line a different sample)

    chr pos ref alt
    1 200 A C
    1 200 A T
    1 200 A -
    1 200 A TT

    Different mutations happen in same coordinates. Are thos mutationes going to be treated as the same? I think I want to have recurrent genes and recurrent positions.

    Thanks

  • #2
    You should try 'bcftools merge'



    By default it will merge you're samples like this:
    1 200 A C,T,-,TT

    But you can tweak the -m parameter in order to get different results.
    Good luck

    Comment


    • #3
      Thanks

      I did some test and as you said that is what vcf-merge does.

      I've alse checked bcftools merge, but as the input paramters are almost the same I used vcf-merge.

      Is it worthy to use bcftools over vcf-merg?

      Thaks

      Comment


      • #4
        I've heard that bcftools is far faster than vcftools, though I've not personally used either of them...

        Comment

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