plink merge vcf files error

[Dung Tran]

Hi, 

I want to merge multiple VCF files (different sample ID) using plink merge. I wonder do I need to convert VCF files to PLINK files before merging? I run the code below and got error: "Fail to open .fam file"

My code is: 

"plink --merge-list {list of vcf files} --out {output} --recode vcf bgz"

Please help! 

Thank you,

Dung

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[Christopher Chang]

From the --merge-list documentation:

"- If a line contains only one name, it is assumed to be the prefix for a binary fileset.
- If a line contains exactly two names, they are assumed to be the full filenames for a text fileset (.ped, then .map). These filesets may not contain multi-character alleles.
- If a line contains exactly three names, they are assumed to be the full filenames for a binary fileset (.bed, then .bim, then .fam)."

Nowhere does it say that VCF files are supported.  You need to convert them to PLINK-format first.