Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • How to view only the variants that are present in multiple VCF files?

    Suppose I have 10 .vcf files and I want to generate a .vcf file that only contains the common variants that are present in all of the 10 files. Can I use GATK CombineVariants followed by SelectVariants intersection to achieve this? Is there another way?

    Thank you

    "If you want to extract just the records in common between two VCFs, you would first run CombineVariants on the two files to generate a single VCF and then run SelectVariants to extract the common records with -select 'set == "Intersection"', as worked out in the detailed example in the documentation guide."


  • #2
    VCFtools: http://vcftools.sourceforge.net/perl....html#vcf-isec

    Comment


    • #3
      I tried vcf-isec and it did not seem to work.

      I was eventually able to install and setup vcftools, including sorting, indexing, and compressing the vcf files with tabix and bgzip.

      The vcf-isec command gave a warning that column names do not match (i.e. 1-Normal and 1-Tumor). The command ran, but the output vcf file was 28 bytes of unreadable characters. Each of the 11 input files are around 80kb.

      These are vcf files generated using MuTect (for comparing tumor to normal samples).

      I am not sure if vcf-isec will work with MuTect vcf files or if there is something I am doing wrong. Maybe I can process the files ahead of time to get them to work.

      The idea is that MuTect gives a list of somatic mutations in cancer samples by comparing to matched normal samples. What I am trying to do is take several MuTect vcf files, and see which variants are present in multiple vcf files or the 'intersection.'

      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, 03-27-2024, 06:37 PM
      0 responses
      13 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-27-2024, 06:07 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      53 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      69 views
      0 likes
      Last Post seqadmin  
      Working...
      X