Question: How to update Family ID in bed file
gravatar for rajneeshpaliwal
2.7 years ago by
rajneeshpaliwal0 wrote:

Hi, I am new user for plink. I have a PED file with Individual IDs for both Family IDs (FID) and individual ID. But now I have known Family IDs and want to update it in plink using --update-ids option in my bed file. I have been using, for this, --update-ids but it updated only for first individual while rest all 1460 individual have same individual ID (IID) at both column of FID and IIDin . Here is the log file message and FAM file result for few starting lines including first FID updated line. How could I do this for all. Is there any other method using awk script?

Log file used PLINK v1.90b3.38 64-bit (7 Jun 2016) Options in effect: --bfile UNIQUES --make-bed --out mydata3 --update-ids recoded.txt

Hostname: hotspot.local
Working directory: /Users/Rpaliwal/Documents/GBSvcfSNPs/PLink_test/FamilyIDcopy
Start time: Thu Aug  4 17:28:47 2016

Random number seed: 1470328127
16384 MB RAM detected; reserving 8192 MB for main workspace.
76395 variants loaded from .bim file.
1462 people (0 males, 0 females, 1462 ambiguous) loaded from .fam.
Ambiguous sex IDs written to mydata3.nosex .
--update-ids: 1 person updated.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 1462 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.852246.
76395 variants and 1462 people pass filters and QC.
Note: No phenotypes present.
--make-bed to mydata3.bed + mydata3.bim + mydata3.fam ... done.

Resulted FAM file

FAM8 DRC_083:250228052 0 0 0 -9
DRC_021:250227990 DRC_021:250227990 0 0 0 -9
DRC_012:250227981 DRC_012:250227981 0 0 0 -9
DRC_030:250227999 DRC_030:250227999 0 0 0 -9
DRC_038:250228007 DRC_038:250228007 0 0 0 -9
DRC_074:250228043 DRC_074:250228043 0 0 0 -9
DRC_047:250228016 DRC_047:250228016 0 0 0 -9
DRC_093:250228062 DRC_093:250228062 0 0 0 -9
.........1400 ids

Looking urgent help Thanks. rajneesh

software error • 1.4k views
ADD COMMENTlink modified 2.7 years ago by genomax65k • written 2.7 years ago by rajneeshpaliwal0
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