Johnlees Seer Versions Save

This includes gzstream as a submodule, and will be the version released under bioconda

This release adds the following features and fixes

• Adds the likelihood ratio test (LRT) as the default p-value for binary traits (issue #42). This has higher power when effect sizes are large.
• Ensure consistency of sample order when using mash rather than kmds. Previous releases will have assumed mash ordering was the same as seer; the .samples file is written correctly by the perl script and mitigates this.
• Fix for the t-test in continuous traits, which could give incorrect p-values for negative effect sizes (issue #46).
• Check for header with filter_seer and map_back

If using mash rather than kmds, please use this release or later.

Adds

• Replaces kmds with mash (but kmds still possible)
• Normalise k-mer distances (as in manuscript)
• New R script functionality plotting (issue #18)
• Fixes issues #28, #29, #30, #32, #33, #34
• map_back and filter_seer updated and bugs fixed
• Add travis-ci

The features are as in the published manuscript, or higher

Adds:

• unit tests
• information about covariates
• invokes Firth regression more often
• doesn't die on failed matrix inversions
• checks for consistency of sample names
• update and addition of some helper scripts

Fixes bug in v1.0.1 where .pheno file was assumed to be sorted. Do not use previous releases, but see v1.0.1 for more release notes

Compile instructions are in README.md. Other information (usage, troubleshooting) is in the wiki

Additions from v1.0.0

• Faster with continuous phenotypes
• map_back and filter_seer consistent with output
• General clean up

Pre-compiled binaries for linux_64 are provided. Use the dynamic version with gcc-4.9 or above, and the dependencies installed. If this isn't possible, use the static version

First version of seer. Instructions to compile are at the start of README.md, and usage follows

Pre-compiled binaries for linux_64 are provided. Use the dynamic version with gcc-4.9 or above, and the dependencies installed. If this isn't possible, use the static version