I've been testing somalier for relatedness and also sex inference.
I have some questions regarding sex and relatedness.
Sex inference:
I've noticed that in some samples, the results for sex inference follow the formulas in (https://github.com/brentp/somalier/issues/125)
but the result is not 'translated' in the sex column (inferred sex) of the somalier.samples file.
e.g.
sex phenotype X_depth_mean X_het X_hom_alt
-1 unknown 17.45 1 162
and the formula is --> if stats[i].x_het / stats[i].x_hom_alt < 0.05 and stats[i].x_dp.n > 10:
The results should be male, am I correct?
The 'x_dp.n' variable is the 'X_depth_mean' in the samples.tsv?
Or do you take into account other parameters?
Relatedness
Regarding relatedness, I've noticed that in "https://github.com/brentp/somalier/wiki/pedigree-inference" to infer the relationships of the samples, you need a minimum of 3 samples "a trio", have relatedness value between 0.4 and 0.6 to $sample, have IBS0 / IBS2 < 0.005 to $sample, and also that the parents can't have a relatedness higher than 0.06.
Hello,
I've been testing somalier for relatedness and also sex inference.
I have some questions regarding sex and relatedness.
e.g. sex phenotype X_depth_mean X_het X_hom_alt -1 unknown 17.45 1 162
and the formula is --> if stats[i].x_het / stats[i].x_hom_alt < 0.05 and stats[i].x_dp.n > 10:
The results should be male, am I correct? The 'x_dp.n' variable is the 'X_depth_mean' in the samples.tsv? Or do you take into account other parameters?
Regarding relatedness, I've noticed that in "https://github.com/brentp/somalier/wiki/pedigree-inference" to infer the relationships of the samples, you need a minimum of 3 samples "a trio", have relatedness value between 0.4 and 0.6 to $sample, have IBS0 / IBS2 < 0.005 to $sample, and also that the parents can't have a relatedness higher than 0.06.
Why the 0.06 is needed?
Thanks in advance!
Arnau