Additional Variant Callers

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ExpansionHunter — Short repeats (eg, TGATGATGA) occur in many places in the human genome, and mutations have been observed where the number of repeats increases (repeat expansions). Such mutations have been associated with some diseases, such as Fragile X syndrome. The tool ExpansionHunter looks for repeat expansions at several positions of interest.

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HLATyper — The human leukocyte antigen region contains genes that play an important role in the human immune system and are used to look for matches for organ transplants. The resequencing workflow uses Isas HLA-Typer to generate likely HLA types for the sample. The output is a tab delimited text file with 4 columns: GeneName, Allele1, Allele2, Rank. The output file lists the 10 most likely pairs of alleles for each of 6 HLA genes.

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ROHcaller — ROH / consanguinity calling identifies the runs of homozygosity (ROHs) from the whole genome SNV variant call set. It then uses the called ROH regions to predict the most likely relationship(s) of the sequenced individual's parents.

For Research Use Only. Not for use in diagnostic procedures.