PLINK2 handle NON_REF in ALT allele column of VCF

[Gourab Saha]

Hi,

I am new to PLINK. The merged VCF I am using contains some rows with NON_REF calls in the ALT allele. For the same row GT value is 0/0. Does PLINK consider those calls as homozygous reference or it excludes those from analysis?



Thanks
Gourab
CONFIDENTIALITY NOTICE: This E-Mail is intended only for the individual or entity to which it is addressed and may contain information that is confidential. If you have received this communication in error, do not distribute. Please delete the original message and immediately notify the sender.

[Chris Chang]

There is no special handling of "NON_REF" allele codes; they are treated as homozygous reference.

--
You received this message because you are subscribed to the Google Groups "plink2-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to plink2-users...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/plink2-users/c138485a-7a93-407a-a3f2-869ca16ce411n%40googlegroups.com.

[Gourab Saha]

Thank you so much for quick answer.

In that regard i have another doubt. 

Currently I am merging my VCF files using BCFtools. But BCFtool is treating those NON_REF as a variant and recording corresponding 0/0 genotype. With PLINK2 can I merge vcf files as --bmerge option is not there? If yes which function do that and as you mentioned in this case PLINK2 wont treat NON_REF as a individual variant at that position right?

I know this sound little complex. It would be great help if you give a resolution to this.


Thanks 
Gourab