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GEMINI roh (version 0.20.1)

GEMINI database:

Only files with version 0.20.1 are accepted.

Minimum number of expected homozygous SNPs:

default: 25

The minimum overall sequencing depth required for a SNP to be considered:

default: 20

The minimum required sequencing depth underlying a given sample's genotype for a SNP to be considered:

default: 0

Minimum run size in base pairs:

default: 100000

Maximum number of allowed hets in the run:

default: 1

Maximum number of allowed unknowns in the run:

default: 3

Comma separated list of samples to screen for ROHs:

e.g. S120,S450

What it does

Runs of homozygosity are long stretches of homozygous genotypes that reflect segments shared identically by descent and are a result of consanguinity or natural selection. Consanguinity elevates the occurrence of rare recessive diseases (e.g. cystic fibrosis) that represent homozygotes for strongly deleterious mutations. Hence, the identification of these runs holds medical value.

The 'roh' tool in GEMINI returns runs of homozygosity identified in whole genome data. The tool basically looks at every homozygous position on the chromosome as a possible start site for the run and looks for those that could give rise to a potentially long stretch of homozygous genotypes.

For e.g. for the given example allowing 1 HET genotype (h) and 2 UKW genotypes (u) the possible roh runs (H) would be:

genotype_run = H H H H h H H H H u H H H H H u H H H H H H H h H H H H H h H H H H H
roh_run1     = H H H H h H H H H u H H H H H u H H H H H H H
roh_run2     =           H H H H u H H H H H u H H H H H H H h H H H H H
roh_run3     =                     H H H H H u H H H H H H H h H H H H H
roh_run4     =                                 H H H H H H H h H H H H H

roh returned for --min-snps = 20 would be:

roh_run1     = H H H H h H H H H u H H H H H u H H H H H H H
roh_run2     =           H H H H u H H H H H u H H H H H H H h H H H H H

As you can see, the immediate homozygous position right of a break (h or u) would be the possible start of a new roh run and genotypes to the left of a break are pruned since they cannot be part of a longer run than we have seen before.