Raremetal Incoming updates
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Finished in test version
- Optimization for unbalanced studies (Jingjing Yang)
- Reduce running time when reading over 10,000s individual genotype from vcf
- A seg fault: sometimes you only have very few variants but raremetal still tries to calculate GC.
- This has been fixed on CSG cluster but not in 4.13.8 release.
Incoming update
- Take snpeff as annotation input
- When no conditional variant is available, warning is generated but not written to log file.
- SKAT conditional analysis misses the last 3 column names. They should be cond_statistics, cond_pvalue_davis, cond_p_value_liu.
- enable reading from .gz annotated vcf
- add SKAT-O
- solve the numeric issue of lambda = 0 in SKAT
- In conditional analysis, when cov matrix between the test variant and its conditioned variants is not invertible, MathSVD still tries to invert that matrix and that leads to weird conditional p values.
