Sample ID ERROR in converting dosage file (.txt) to VCF in PLINK 2.0
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6 weeks ago
pateap0 • 0

Hi, I have a dosage file (.txt format; alternative allele count 0-2) that I would like to convert to a VCF through PLINK 2.0 but am running into sample ID issues.

I am attempting the following code block;

plink2 --import-dosage dosage_file.txt format=1 chr-col-num=1 pos-col-num=2 skip0=2 skip1=0 skip2=0 --psam sampleinfo.psam --keep-allele-order --recode vcf id-paste=iid --out output

'dosage_file.txt' has a header with sample IDs (column names) 'sampleinfo.psam' has a header starting with #IID and has the corresponding sample IDs to the dosage file (I checked this)

However, I run into the following error:

Error: .fam file does not contain all sample IDs in dosage file. End time: Sun Oct 17 20:14:16 2021

My sample IDs are in the form of "BCAC-#######" where # represents a string of numbers. Not sure if this matters.

Would anyone have any insight into the matter?

PLINK2.0 VCF dosage • 148 views
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