I'm trying to run plink2's --make-king-table command.
However, upon running
~/programs/plink2 --bcf 1000genomes.bcf --make-king-table --out plink2.king --psam .1000g.tsv
I get an error:
Error: Mismatched IDs between --bcf file and condon.1000g.tsv.
so I made a psam file looking like:
NA21127 1
NA21128 1
NA21129 1
NA21130 1
NA21133 1
NA21135 1
NA21137 2
NA21141 2
NA21142 2
NA21143 2
However, this still gives the same errors. I have assured that the IDs are in the same order. I don't understand how this psam file should be put together, nor can I find documentation on it.
How can I make this psam file?
1 answer
SOLUTION, ironically, from Grok:
Example .psam File Here’s an example of a simple .psam file with just the required column:
#IID
SAMPLE1
SAMPLE2
SAMPLE3
Here’s a more detailed example including optional columns:
#FID IID PAT MAT SEX
FAM1 IND1 0 0 1
FAM1 IND2 IND1 IND3 2
FAM2 IND4 0 0 0
In this example: FID groups individuals into families (FAM1, FAM2). IID is the unique individual ID. PAT and MAT specify parents (0 if unknown). SEX is coded as 1 (male), 2 (female), or 0 (unknown).
since I don't know family IDs, I add a header '#IID SEX' to the psam file, and that was it
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https://www.cog-genomics.org/plink/2.0/formats#psam
thank you, that didn't show up on Google searches. Time would've been saved if this error had a helpful error message.