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A minor new release addresses some issues with VCF parsing, and provides incremental speed improvements.
This release is a minor fix to v1.2 and addresses a couple of VEP annotation (native output) format bugs. A secondary output file (.excluded) now lists variants excluded from the main output file due to lack of VEP annotation. Also, sites with 2+ alternate alleles will be reported in multiple lines (one per alternate allele) when VEP native output format is provided.
We fixed a bug related to segmentation scoring, added broader VEP output format compatibility, and enabled preliminary recessive scoring functionality for the "score" subcommand.
If you use MendelScan to aid your research, please cite the publication:
Koboldt DC, Larson DE, Sullivan LS, Bowne SJ, Steinberg KM, et al. Exome-based mapping and variant prioritization for inherited Mendelian disorders. Am J Hum Genet. doi:10.1016/j.ajhg.2014.01.016
This is the initial release of MendelScan, a software package for analyzing variants identified by family-based sequencing of rare genetic diseases. There are three main functions included with this release:
java -jar MendelScan.jar score -- prioritize variants in a VCF based upon segregation, annotation, population frequency, and gene expression
java -jar MendelScan.jar rhro -- apply rare heterozygote rule out to map dominant disease genes
java -jar MendelScan.jar sibd -- apply shared IBD analysis to map disease genes
A manuscript describing this tool has been submitted; in the interim, please cite MendelScan by noting the version number and citing its home URL: http://gmt.genome.wustl.edu/mendelscan.