Some useful metrics are provided in the Sample/Analysis information option
Sex Prediction
As part of the main analysis, the sample sex is predicted based on zygosity in selected chromosome X SNVs. The algorithm assumes that females are XX and males are XY. Sex is predicted with a p-value (binomial test) <0.01, otherwise sex is undetermined. INDELs are not considered in the calculation due to their higher false positive rate.
Homozygosity Count
This metric provides the fraction of rare variants in homozygosity. A minimum of 50 genotypes are required to report results.
- An SNV is considered rare when its frequency is below 1% or if it is unknown.
- InDels are not considered in the calculation due to their higher false positive rate.
The number of rare SNVs and their fraction in homozygosity is reported.
Runs of Homozygosity
Analyses are scanned for presence of extended segments of autozygosity. Runs of homozygosity (ROH) are computed directly from the VCF file. Calculations are based on input VCF with FORMAT columns containing either genotype likelihoods (PL) or genotypes (GT). By default, genotype likelihoods are expected. ROH is thresholded for lengths: 100Kb, 500Kb, 1,5Mb, 5Mb. Please note:
- ROH is computed for germline samples, but not for somatic
- Only bi-allelic sites are considered in ROH calculations.
- Only ROH in autosomal chromosomes is reported.
- All ROH have a minimum of 50 variants
- INDELs are not considered in the calculation due to their higher false positive rate.
- Minimum ROH quality (Phred score) is 20. ROH quality represents the probability of the state assignment being incorrect. Bigger values indicate a more confident call.
- ROH is calculated for all WGS, WES and panel assay analyses. Calls for panel are unreliable due to sparsity of target regions.
The following metrics are tabulated for each length threshold:
NROH: The number of ROH sections detected in the sample
SROH: The total length of ROH in bp
maxROH: The length of longest ROH segment in bp
FROH: The fraction of autosomal genome in autozygosity