Log of Odds (LoD) score

LoD score means the probability of observing the genotypes in the family are linked or not with the target binary trait. WISARD provides a simple function to calculate LoD score by using --lod option.

Computing LoD score

C:\Users\WISARD> wisard --bed test_miss0.bed --lod

NOTE!

Currently, only the computation of single-point LoD score is supported!

Interpretation of LoD score [top]

Since LoD score is based on the minus logarithm of 10, Higher positive score means that the observed genotypes are highly unlikely occured by chance. In same manner, higher negative score means that it can be occured by chance, which indicates there is no linkage.

In general, a LoD score greater than 3.0 can be interpreted as evident linkage, and can be possible sign of linkage if the score is greater than 1.73. In contrast, the score less than -2.0 can be regarded as the sign of no linkage.

Output files [top]

Meaning of each column in [prefix].lod.res

lod.res is...			A result of Log of Odds analysis (TSV)
Column	Format	Modifier	Description
CHR	real	NONE	Estimated inbreeding coefficient
VARIANT	real	NONE	Estimated inbreeding coefficient
POS	real	NONE	Estimated inbreeding coefficient
ALT	real	NONE	Estimated inbreeding coefficient
ANNOT	real	NONE	Estimated inbreeding coefficient
LOD	real	NONE	Estimated Log of Odds
R	real	NONE	Estimated R

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