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Problem creating STRUCTURE inputs with PLINK

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"
vcf population plink structure genetics
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updated by katherinedrotos • katherinedrotos • written by Begonia_pavonina • Begonia_pavonina

Provide the error message.

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written by Arup Ghosh Arup Ghosh

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.

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written by katherinedrotos • katherinedrotos

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