SnpSift Private

Annotate if a variant is private to a family.

A Private=Family_ID is added to a variant's INFO field, if the variant is only found in one family. A TFAM file (see PLINK's documentation) specifies a mapping from sample IDs to family IDs.

E.g.:

$ java -jar SnpSift.jar private pheotypes.tfam imp.ann.vcf > imp.ann.private.vcf

An annotated variant may look like this:

1   1005806 rs3934834   C   T   .   PASS    AF=0.091;..;Private=Family_47

This indicates that the variant is only found in members of Family_47, according to the definitions in pheotypes.tfam.