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
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
•
written
by
Pierre Lindenbaum
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.
put your pedigree in a database (e.g. sqlite3 ).
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