Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Strange Fst distribution in BayeScan

    I have used BayeScan (2.1) successfully several times on various subsets of a large SNP dataset that I am currently working on. Recently, I tried to use it to infer outliers between several population pairs using my whole dataset (57,000 SNPs), and came up with a peculiar result in all 9 population pairs. The plot of posterior density for Fst looks as expected, except with a mean Fst ~ 0.4 - 0.6, depending on the population pair (not ~0.05 as I know them to be). If I plot a frequency distribution of Fst values inferred by BayeScan, the distribution is the opposite of what I would expect -- the highest frequency is Fst at these high values around 0.5, with a tail on the left for low Fst values. These are bird populations that we know are differentiated but still experience some gene flow, and are geographically quite close. Calculating Fst in vcftools or Genepop gives a mean and distribution more in line with expectations -- mean ~0.05 with a tail to the right of higher Fst values.

    Has anyone else experienced something similar? I have been picking my brain to try to figure out what is causing this to happen, but don't have any hypotheses yet. The current dataset has less missing data than subsets I have previously used, so I wouldn't expect that to be an explanation, and I used the same approach as previously. I used PGDSpider to convert from vcf format to BayeScan format.

    I would appreciate any thoughts!

  • #2
    For reference

    cross-posted on Biostars: https://www.biostars.org/p/160738/

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Latest Developments in Precision Medicine
      by seqadmin



      Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

      Somatic Genomics
      “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
      Yesterday, 01:16 PM
    • 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

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 07:15 AM
    0 responses
    13 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 10:28 AM
    0 responses
    17 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 07:35 AM
    0 responses
    20 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-22-2024, 02:06 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Working...
    X