Using ANNOVAR summary routine I have got a exome_summary.csv file that contains different columns with 1000 genomes and 5400 exomes frequencies with some empty cells. I asume that empty cells correspond to SNPs that were not found in any of these databases. However there are cases where you get frequencies either in 1000 genomes or 5400 exomes but not in the other database. I would understand it if the alllele frequency in the alternate database would be very low, but there are cases where this frequency can be up to 80%. Does anyone know what is the reason for these big discrepancies between these databases?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
The 1000G and 5400ESP projects used different pipelines for sequencing, read mapping and and variant calling, so at least some of the major discrepancies between the listed allele frequencies are due to different quirks in their respective pipelines. For example, each pipeline might consistently map ambiguous reads to a different site in a repetitive or low-complexity region, giving the variant calls in that region a high frequency in one database but not the other.
Latest Articles
Collapse
-
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...-
Channel: Articles
05-06-2024, 07:48 AM -
-
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...-
Channel: Articles
04-22-2024, 07:01 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 02:46 PM
|
0 responses
11 views
0 likes
|
Last Post
by seqadmin
Yesterday, 02:46 PM
|
||
Started by seqadmin, 05-07-2024, 06:57 AM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
05-07-2024, 06:57 AM
|
||
Started by seqadmin, 05-06-2024, 07:17 AM
|
0 responses
17 views
0 likes
|
Last Post
by seqadmin
05-06-2024, 07:17 AM
|
||
Started by seqadmin, 05-02-2024, 08:06 AM
|
0 responses
23 views
0 likes
|
Last Post
by seqadmin
05-02-2024, 08:06 AM
|
Comment