Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • SNPsaurus
    replied
    vcftools has a --thin option for removing SNPs that are too close.
    It also has a --max-maf for setting the maximum allowable minor-allele frequency. So setting that to 21% should give you SNPs that are in a single individual.

    After that, a custom script, or Excel :-( would extract the SNPs specific for each individual, or maybe use http://snpeff.sourceforge.net/SnpSift.html ? I'm not so familiar with it but it seems like it could do what you ask.

    Leave a comment:


  • JdeBruin
    started a topic bcftools for finding unique SNP

    bcftools for finding unique SNP

    Hi,

    Would appreciated some help, I am a neophyte when it comes to dealing with vcf files.

    I have 5 vcf files each represented a unique individual of the same species. I would like to filter the vcf's for snps that are unique to each individual thus ending with 5 vcf one for each individual contain snp not found in any of the other vcf files. Secondly I would like to setup a filter that removes SNPs that are with 36bases of each other.

    I have been using vcftools and bcftools to try and achieve the above for the unique part I have used bcftools isec -n -1 , is this correct ?

    Any help would be appreciated.

Latest Articles

Collapse

  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM
  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    04-22-2024, 07:01 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 05-14-2024, 07:03 AM
0 responses
20 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-10-2024, 06:35 AM
0 responses
44 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-09-2024, 02:46 PM
0 responses
54 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-07-2024, 06:57 AM
0 responses
42 views
0 likes
Last Post seqadmin  
Working...
X