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PLINK | Updating sex information issue

Hello,

I am attempting to update the sex information of my cohort vcf data by using PLINK.

This is the command I am running:

plink --bed input_bed --bim input_bim --fam input_fam --update-sex input_sex.txt --make-bed ---out output_name > stdout.out

For some reason, I am getting the error in the stdout.out: "--update-sex: 0 people updated, 1066 IDs not present". I realized this may be a mapping issue between the .fam file I am trying to update and my sex.text file. Here's what each of them are:

.fam file (produced from --make-bed and an input vcf file)

0001 1 0 0 0 -9
0002 1 0 0 0 -9
0003 1 0 0 0 -9
0004 1 0 0 0 -9
0005 1 0 0 0 -9
0006 1 0 0 0 -9
0007 1 0 0 0 -9
0008 1 0 0 0 -9
0009 1 0 0 0 -9
0010 1 0 0 0 -9

sex.txt file (produced from the cohort's pedigree file)

FID IID Sex
0001    0001_1  1
0002    0004_1  2
0003    0007_1  1
0004    0010_1  1
0005    0015_1  1
0006    0016_1  2
0008    0022_1  2
0010    0028_1  2

What is going wrong here? And how could I fix it?

Thank you, I really appreciate any help.

plink
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updated by alpha • alpha • written by S • S

I also think an issue may be in the initial making of the .fam file from --make-bed from the initial vcf file.

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 0001_1 0002_1 0003_1 0004_1 0005_1

This is the headerline with the five sample IDs from the VCF file, once all the bfiles are made, this is the fam file:

0001 1 0 0 0 -9
0002 1 0 0 0 -9
0003 1 0 0 0 -9
0004 1 0 0 0 -9
0005 1 0 0 0 -9

I am unsure why the individual IDs are not kept. Does anyone know?

For reference, in a .fam file the components are Family ID, Individual ID, Paternal ID, Maternal ID, and Sex. Clearly here the individual IDs are wrong (all of them are 1).

Thank you again.

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written by S • S

I believe plink understands underscore "_" as a separator between FID and IID. If you look at your original IDs, they are all numbered and then followed by _1, that's probably why you are encountering same IID. So, I believe solving this issue requires just replacing the xxxx_1 by 1 along the sex.txt file

P.s. I know it's a very old issue (I just signed up here), but I hope others can benefit somehow from the small detail.

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written by alpha • alpha

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