Plink changing sample IDs
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Riana Wernick
Jan 10, 2017, 1:09:38 PM1/10/17
to plink2-users
Hi, I am hoping someone can help me with this.
I am trying to take a vcf file and remove loci that fail a HW test with p <= 0.001 and remove loci missing >5% genotypes.
However, while I can do that, it appears that Plink is renaming my sample IDs. For example, if the original ID is "1234" the new id is "1234_1234".
The code I am writing is:
plink --vcf file_input --make-bed --hwe 0.001 --geno 0.05 --out out_file
Any help would be much appreciated!
I am trying to take a vcf file and remove loci that fail a HW test with p <= 0.001 and remove loci missing >5% genotypes.
However, while I can do that, it appears that Plink is renaming my sample IDs. For example, if the original ID is "1234" the new id is "1234_1234".
The code I am writing is:
plink --vcf file_input --make-bed --hwe 0.001 --geno 0.05 --out out_file
Any help would be much appreciated!
Christopher Chang
Jan 10, 2017, 1:49:52 PM1/10/17
to plink2-users
PLINK 1.x requires both a family ID and an individual-specific ID. However, you can set all the family IDs to '0' by adding "--const-fid 0" to your import command. (See https://www.cog-genomics.org/plink2/input#double_id for a few more options.)
RianaW
Jan 11, 2017, 5:41:47 PM1/11/17
to plink2-users
Thank you, that did the trick!
On Tuesday, January 10, 2017 at 10:09:38 AM UTC-8, RianaW wrote:
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