Problem creating STRUCTURE inputs with PLINK

Question

[Begonia_pavonina]

I have formatting issues when preparing my data for STRUCTURE analysis. I am creating the input files for STRUCTURE, but unfortunately the .strct_in file produced seems to show the samples names, that trigger an error in STRUCTURE. Did anyone had this problem before?

    # Base names for outputs 
    PLINK_BASE="all.work10.pruned" 
    STRUCTURE_BASE="all_for_structure"

    # Step 1: Convert to PLINK format  
plink --vcf "${PLINK_BASE}.vcf.gz" \
              --make-bed --double-id --allow-extra-chr \
              --out "$PLINK_BASE"

# Step 2: Convert to STRUCTURE format  

plink --bfile "$PLINK_BASE" \
              --recode structure --allow-extra-chr \
              --out "$STRUCTURE_BASE"

[Arup Ghosh]

Provide the error message.

[katherinedrotos]

Can you provide the error message and what plink version you are using?

For what it's worth, I've encountered many challenges in getting plink to convert to a format STRUCTURE will accept ... I end up using PGDSpider2 sometimes, especially if I just have a single vcf to convert.