Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • merging VCF files

    Hi all,

    I need to merge multiple VCF files, any idea? I have tried it using VCFtools but it does not work. I get an error message
    -bash: vcf-merge: command not found

    thanks

  • #2
    is your installation directory of vcftools in your $PATH env variable

    Comment


    • #3
      For many of the VCFtools, you also need to bgzip and tabix index VCf files. And Laura is correct, your installation of VCFtools should be in your $PATH env variable as well as exported to your PERL5LIB. It also wouldn't hurt to add bgzip and tabix as well. Just a word of warning though, some of the binary VCFtools do not work so well.
      Alternatively, you could also try to use GATK to merge VCF files. You can find the necessary tool here:
      If you are unable to find something or have a question about our new website, please email [email protected]. For other inquiries related to the Broad Institute, the necessary contact information can be found here.


      Good luck,
      Dameon

      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
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      49 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