Pedigree file information
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Entering edit mode
5.6 years ago
Mani ▴ 20

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 plink pedigree .ped • 3.6k views
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Entering edit mode
5.6 years ago

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

awk '(\$6=="2")' *.ped

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Entering edit mode

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.

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Entering edit mode

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