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Crop Database
germplasm
phenotype
genotype
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gwas
tools
GWAS Analysis Pipeline
v2.10.0
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Rice
database | Change >>
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Genotype
( wgsV2.9.0 )
Setup filtering parameters
Use pre-filtered genotype set
Filter for :
Missing =
MAF =
Filter using :
PLINK
TASSEL
Prunning (by LD) :
r
2
=
Thinning (by distance) :
distance =
k
Select genotype set :
[wgsV2.9.0] Miss 0.1, MAF 0.05
[wgsV2.9.0] Miss 0.2, MAF 0.05
[wgsV2.9.0] Miss 0.3, MAF 0.05
[wgsV2.9.0] Miss 0.1, MAF 0.05, Prune 0.1
[wgsV2.9.0] Miss 0.1, MAF 0.05, Prune 0.1, Thin 1k
[wgsV2.4.1] Miss 0.1, MAF 0.05, Prune 0.1, Thin 1k
* Keep in mind that missing and MAF are not filtered according to your phenotypes
Phenotype
Upload
Download example file
here
GWAS Software
rTASSEL
TASSEL
GWAS Method
Single-locus
GLM
MLM
CMLM
SUPER
Multi-locus
MLMM
FarmCPU
BLINK
GAPIT Parameters
PCA.total =
* To observe PCA before setting parameter,
you can
run PCA analysis here
* To observe PCA before setting parameter,
see PCA of pre-filtered genotype here
Submit
Refresh
10
Queue
Creating job
...
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Each job will stay in this list for 5 days, unless you delete it
Result
X
X
Share result
Copy this url to share
X
To export track data in current region ...
1) Find "Save track data" on the track menu
2) Select options and click "Save"
GFF3 format is recommended for gene annotation, while BED format is recommended for a quick overview on position and IDs
Close
X
PCA
Run
Starting
Please login to BMS
Username
Password
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