Question: Annovar and CADD Annotation
1
gravatar for Ishtiaq Ahmad Khan
4.6 years ago by
Pakistan
Ishtiaq Ahmad Khan60 wrote:

I CADD scored my set of variants called on build 38 by using Annovar. Then I converted my coordinates to hg19 by crossmap and liftover separately and scored them using CADD database and script. The output is quite different. I double checked my coordinate conversion and it is fine. But CADD server and annovar giving different scores. Kindly explain a bit.

snp • 2.2k views
ADD COMMENTlink modified 4.6 years ago by Vivek2.4k • written 4.6 years ago by Ishtiaq Ahmad Khan60

Here is a comparison of CADD scores (build 19) for different versions. Why it is so different some time??

CHROM#  Position   REF  Alt  V1.0   V1.1   V1.2   V1.3
1       12854074   C    A    14.29  23     22.4   23.5
1       17301446   G    C    14.3   21.6   19.85  20.8
1       20073719   G    A    17.55  24.9   23.9   25.2
1       22222455   G    T    14.08  11.21  12.46  8.884
1       23966983   G    A    14.2   23.1   22.7   23.3
1       25747156   T    C    13.08  1.574  2.434  9.396
1       45795084   G    A    7.869  11.74  10.95  16.82
1       45974478   G    A    29.2   22.8   22.4   32
1       62579891   G    T    25.5   29.1   28.7   29.4
1       66081833   C    G    13.58  24.9   24     24.7
1       94564483   C    T    24.1   25.3   24.2   24.9
1       109365991  C    T    9.386  21.7   24     23.2
1       148580684  G    A    0.969  0.014  0.014  0.063
1       150483966  G    A    22.3   22.2   22.2   32

ADD REPLYlink modified 3 months ago by RamRS25k • written 4.6 years ago by Ishtiaq Ahmad Khan60
0
gravatar for Vivek
4.6 years ago by
Vivek2.4k
Denmark
Vivek2.4k wrote:

The correlation between CADD scores for the same set of variants over different versions of the CADD release are rather low, especially between version 1.0 and latter versions. You can see the plots from the release notes:

http://cadd.gs.washington.edu/static/ReleaseNotes_CADD_v1.2.pdf

There are differences between the regression models used between the versions as well as updating the feature annotation set used to derive the scores.

ADD COMMENTlink modified 3 months ago by RamRS25k • written 4.6 years ago by Vivek2.4k
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