Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:37 PM
        0 responses
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        9 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        50 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        67 views
        0 likes
        Last Post seqadmin  
        Working...
        X