Plink1.9 and g.vcf vs vcf

[Brittany Whitt]

Hi all! 

I have not seen much information about this elsewhere and was curious if anyone could help clarify. I want to use multiple files (whether they are merged or not depends on whether the input into plink needs to be a vcf or if it can read g.vcf) and output them into plink format. I have not seen much about g.vcf format and plink, but was wondering if anyone has used it and gotten it to work or if it is something that needs to be converted into vcf format to begin with. 

My other option would be to take the individual vcf files for my samples and run them through one by one. Again, it would be nice to have all of the information included in a g.vcf, especially when it comes to the genotypes present, but I am unsure of how to proceed. 

I can definitely elaborate on the issue where clarification is needed, but I would appreciate any and all input!

[Christopher Chang]

If you are referring to the "gVCF" format, plink does not directly support it for now.  You'll want to use another tool to convert gVCFs to regular VCF files containing all variants of interest.