Question: Pedigree file information
0
gravatar for Mani
4.0 years ago by
Mani20
Jeddah
Mani20 wrote:

Hi,

I have few plink pedigree files with me. I want to retrieve data from the file such as Father, mother and siblings etc.

I understand the data is in the Format;

Family ID, Individual ID, Paternal ID, Maternal ID, sex, Phenotype

Is there any script or tool to draw the pedigree chart upon providing the .ped files as input and also for providing information on the .ped files such as;

FAM001  Individual1  0 0  1  2

FAM001  Individual2  0 0  2  1

FAM001  Individual3  Individual1  Individual2   1 2

FAM001  Individual4  Individual1  Individual2   2 1

 

Parents:

Individual1

Individual2

Offspring:

Individual3

Individual4

Affected:

Individual1

Individual3

 

I can do this manually for few files but I have more than 100 files and need to classify them like above. Any help would be appreciated.


~Thanks

.ped ped plink pedigree • 2.6k views
ADD COMMENTlink modified 4.0 years ago by Pierre Lindenbaum124k • written 4.0 years ago by Mani20
2
gravatar for Pierre Lindenbaum
4.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:

drawing : https://madeline.med.umich.edu/madeline/webservice.php  , a awk script Visualizing Pedigrees From Plink Files  , ...

 

"input and also for providing information on the .ped files such as;" : use awk ? e.g: affected:

awk '($6=="2")' *.ped
ADD COMMENTlink written 4.0 years ago by Pierre Lindenbaum124k

Thank you Pierre Lindenbaum, the plotting part is solved thank to your previous post.

The problem is the above awk statement can give information on people with disease status 2. But I also require the relationship information between the individuals in the family. SO I can directly compare data within the family, ex father and mother data with offspring and vice versa.

 

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Mani20

put your pedigree in a database (e.g. sqlite3 ).

ADD REPLYlink written 4.0 years ago by Pierre Lindenbaum124k
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