Galaxy |

GEMINI comp_hets (version 0.18.1.1)

GEMINI database:

Only files with version 0.18.1 are accepted.

Columns to include in the report:

By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns.

Apply additional constraints:

By default, this tool will report all variants regardless of their putative functional impact. In order to apply additional constraints on the variants returned, you can this optional filter.

The min. number of kindreds that must have a candidate variant in a gene:

default: 1 (--min-kindreds)

Comma seperated list of families to restrict the analysis to.:

e.g. Family1,Family3 (--families)

Report candidates that also impact samples labeled as unaffected.:

(--allow-unaffected)

The minimum aligned sequence depth (genotype DP) required for each sample:

default: 0 (-d)

The minimum genotype quality required for each sample in a family.:

default: 0 (--min-gq)

The maximum phred-scaled genotype (PL) allowed for each sample in a family.:

default: -1 not set (--gt-pl-max)

Find compound hets by inheritance pattern, without regard to affection:

(--pattern-only)

Default is to show only confident compound hets. Set to 2 or higher to include pairs that are less likely true comp-hets.:

default: 1 (--max-priority)

What it does

Many recessive disorders are caused by compound heterozygotes. Unlike canonical recessive sites where the same recessive allele is inherited from both parents at the _same_ site in the gene, compound heterozygotes occur when the individual’s phenotype is caused by two heterozygous recessive alleles at _different_ sites in a particular gene.

So basically, we are looking for two (typically loss-of-function (LoF)) heterozygous variants impacting the same gene at different loci. The complicating factor is that this is _recessive_ and as such, we must also require that the consequential alleles at each heterozygous site were inherited on different chromosomes (one from each parent). As such, in order to use this tool, we require that all variants are phased. Once this has been done, the comp_hets tool will provide a report of candidate compound heterozygotes for each sample/gene.