Unable to pass Gender file using --update-sex parameter with M and F coding

[Abhishek Shakya]

Hi,

I am trying to convert a BGZIP file to binary fileset using following command:

plink2 --bcf test.vcf.gz --sort-vars --set-missing-var-ids @:#:\$r,\$a --new-id-max-allele-len 487 --update-sex /data/sample_sex_map.csv --make-pgen vzs --out output

However, I got an error:

Error: Line 2 of --update-sex file has fewer tokens than expected. 

Here is my sample_sex_map.csv file looks like

#IID,SEX
sample1,F
sample2,M

Question:

• Do I have to change M and F to 1 and 2?
• The documentation says it supports both: https://www.cog-genomics.org/plink/2.0/data#update_indiv
  

PS: I am attaching the log file with dummified paths.

[Abhishek Shakya]

Diagnosis:

• I was using csv file(comma separated).
• Plink2.0 doesn't support comma separated files for --psam and --update-sex flag

Solution:

• Use space or tab separated files for updating sex.