Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Allele frequency per ethnic group in 1000 genome project

    Hello,

    I'm trying to figure out the relation between overall allele frequency and the reported allele frequency per ethnic group (i.e., AFR, EUR, ASN) in the 1000 genome project.
    I'm using the following frequency files downloaded from ftp://ftp.1000genomes.ebi.ac.uk/vol1...lease/20100804 (or the 'supporting' sub directory under that path).

    ALL.2of4intersection.20100804.sites.vcf.gz
    AFR.2of4intersection_allele_freq.20100804.sites.vcf.gz
    ASN.2of4intersection_allele_freq.20100804.sites.vcf.gz
    EUR.2of4intersection_allele_freq.20100804.sites.vcf.gz

    There are several issues with the reported frequencies in these file that do not make much sense.
    Below are some examples.

    1. The frequencies for rs112872773 are: AF=0.120, AF_AFR=0.120, AF_ASN=0.120, AF_EUR=0.120 where each frequency is taken from the corresponding file. It is highly unlikely that the allele frequency is exactly the same across all groups.

    2. For rs117704637, the frequencies are: AF=0.005, AF_AFR=0.00, AF_ASN=-1, AF_EUR=0.01, where '-1' indicates that the rsID does not appear in the file. Note that for AF_AFR the rsID does appear but with a frequency of 0.00. So, is there a reason for reporting zero frequency rather than not reporting anything?

    3. For rs9269941 the frequencies are: AF=0.121, AF_AFR=0.06, AF_ASN=0.03, AF_EUR=0.06. Here there is a reported frequency for each group but the overall frequency is higher than any of the group ones.

    I would appreciate any help in clarifying these issues or any other ways I could get that data.

    Thank you very much,

    Izhar

  • #2
    Another bug or feature issue....

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Best Practices for Single-Cell Sequencing Analysis
      by seqadmin



      While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
      06-06-2024, 07:15 AM
    • 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,”...
      05-24-2024, 01:16 PM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 06-17-2024, 06:54 AM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 06-14-2024, 07:24 AM
    0 responses
    21 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 06-13-2024, 08:58 AM
    0 responses
    17 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 06-12-2024, 02:20 PM
    0 responses
    20 views
    0 likes
    Last Post seqadmin  
    Working...
    X