Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Annotation of SNPs

    Sorry if this is a really obvious question - I feel like there has to be an easy answer that I am just overlooking. I've used SAMtools mpileup to call SNPs in my RNAseq data. The SNPs are then listed by chromosome and position. How do annotate them so that the gene and whether they are intronic or exonic is matched with the SNP?

    Thanks for any help you all can give me!

  • #2
    Wise enough not to reinvent the wheel and try the following tools:

    snpEff http://snpeff.sourceforge.net/
    annovar http://www.openbioinformatics.org/annovar/


    snpEff has a larger choice of reference annotation databases and supports the pileup format. It also supports VCF format.



    Originally posted by mgibson View Post
    Sorry if this is a really obvious question - I feel like there has to be an easy answer that I am just overlooking. I've used SAMtools mpileup to call SNPs in my RNAseq data. The SNPs are then listed by chromosome and position. How do annotate them so that the gene and whether they are intronic or exonic is matched with the SNP?

    Thanks for any help you all can give me!

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Exploring the Dynamics of the Tumor Microenvironment
      by seqadmin




      The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
      07-08-2024, 03:19 PM
    • seqadmin
      Exploring Human Diversity Through Large-Scale Omics
      by seqadmin


      In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
      06-25-2024, 06:43 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 07-19-2024, 07:20 AM
    0 responses
    141 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-16-2024, 05:49 AM
    0 responses
    116 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-15-2024, 06:53 AM
    0 responses
    109 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-10-2024, 07:30 AM
    0 responses
    43 views
    0 likes
    Last Post seqadmin  
    Working...
    X