Kinship Formats

The new format for storing kinships uses three files: sample IDs are stored in the text file with extension grm.id; kinships are stored in the binary file with extension grm.bin; and counts in the binary file with extension grm.N.bin. When calculating kinships, the option –kinship-gz allows you to save kinships in a gzipped file, while with –kinship-raw you can save these as a large text matrix.

Previously, the default was to save kinships and counts in a single file, with extension either grm.gz or grm.cont. If you have a kinship matrix stored in this format, LDAK can convert to the new format:

–convert-gz <output> –grm <kinfile>

This will search for a kinship file with extension grm, so if stored as grm.gz, first gunzip, or if stored as grm.cont then rename. Alternatively, LDAK can convert kinships stored in a large square matrix:

–convert-raw <output> –grm <kinfile>

This will look for a kinship file with extension grm.raw. In both cases, the kinships will be resaved in the files <output>.id, <output>.bin and <output>.N.bin.