GEVALT accepts input in a variety of formats. Genotype data can be loaded as unphased genotypes in the standard linkage format, or as either partially or fully phased chromosomes. Genotype data dumps from the HapMap website [5] can also be loaded. When using the standard linkage format, the user can specify family structure as well as disease status. The user can also specify marker information, including name and location. Upon loading a dataset, GEVALT first phases the genotypes in the following manner: For data consisting of unrelated individuals, GEVALT uses Gerbil to phase the genotypes. For data consisting of two-generation pedigrees, GEVALT first creates a set of trios, one per family, where each trio contains the child with least missing data. In each trio phasing is done, if possible, according to Mendelian rules. Then only the children's genotypes are phased using Gerbil and each parent's haplotypes are deduced from its child's haplotypes. Gerbil is then run again on the set of the parents' genotypes only to complete the missing data. The haplotypes of the children that were not included in the trios are deduced from their parents' haplotypes.
After phasing is completed, GEVALT generates several displays and option menus including the following:
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Phased genotypes: The phased genotypes of each individual are displayed. Different colors are used to indicate alleles phased by GERBIL, missing data and Mendelian errors (Figure 1). For data consisting of pedigrees, the phased genotypes are divided into two groups, parents and children, and each group is displayed separately.
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Stampa: Select tag SNPs using the Stampa algorithm (Figure 2). The user can specify the desired number of tag SNPs, and the algorithm finds an optimal set of tag SNPs and reports its prediction accuracy. The user can add or remove tag SNPs from the set manually and GEVALT recalculates the prediction accuracy of the new set.
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Individual Stats: Summary statistics for each individual are displayed (Figure 3). These include the percentage of missing genotypes, the percentage of heterozygous markers, the percentage of minor alleles and a tally of Mendelian inheritance errors.
All of Haploview's displays and option menus are available. See [4] for a full description of these features. In addition, the following changes and extensions are introduced:
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Association: GEVALT contains a faster implementation of the permutation test in C++ instead of JAVA. The new implementation runs about 20 times faster than the JAVA implementation in Haploview. In the haplotype associations tab, a p-value is calculated for each block and for each haplotype (Figure 4).
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Haplotypes: The common haplotypes in each block are computed based on the Gerbil solution.
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Check markers: Phasing by Gerbil is done only for the set of picked markers. Whenever the set of picked markers changes, GEVALT recalculates the phasing, and all displays are updated accordingly.
Each of these displays and option menus is shown on a separate tab, allowing the user to move from one to the next. Interactive modifications made by the user in any panel are reflected in all the others. The information on each panel can also be exported to a PNG image file or to a text file. Additionally, the program has a command-line mode, which allows the user to run all the analyses without opening the GUI on one or more files at once.
The running time of GEVALT is dominated primarily by that of Gerbil and Stampa (see the references for detailed reports on the running times of these programs). All other operations, such as parameter adjustments and display changes, are done with no noticeable delay even for data sets with hundreds of markers and hundreds of individuals. Gerbil can currently handle up to 300 markers, while Stampa can handle thousands of markers. Both algorithms can handle thousands of individuals.
To the best of our knowledge, only two extant programs offer both algorithmic and visualization tools for genotype analysis: Haploview [4] and HapScope [6]. As described above, GEVALT maintains the popular, user-friendly interface of Haploview, but replaces its standard EM algorithm for phasing with the Gerbil algorithm. This allows a more accurate estimation of the phased haplotypes and a visualization of each individual's inferred haplotypes (and not just common haplotypes as in Haploview). Besides the Tagger algorithm for tag SNPs selection implemented in Haploview (and also in GEVALT), GEVALT also offers STAMPA, which is not only very efficient, but also allows the user to choose the amount of tag SNPs. Other advantages and improvements over Haploview are listed above. A current limitation of Gerbil is allowing at most 300 markers. We intend to remove this limitation in the future (see below). The HapScope software includes analysis programs and a visualization tool. Most of the analyses are done separately using the command line and the results are then loaded into the visualization tool. In contrast, in GEVALT all the analyses are done within the graphical user interface, which makes it more user friendly and easy to use. HapScope uses PHASE [7] or SNPHAP [8] as its phasing algorithm. PHASE was shown to be slightly more accurate than Gerbil but much slower [1]. In contrast to HapScope, GEVALT facilitates association tests and can handle family structures. On the other hand, only HapScope includes modules for reference sequence annotation, SNP mapping and SNP classification.
We intend to continue the development of GEVALT. In particular, we shall extend Gerbil to handle more SNPs, and improve Stampa so that it incorporates into its solution predefined tag SNPs. We also intend to incorporate a new algorithm for evaluating the significance of disease association, which is dramatically faster than the standard permutation test [9].
