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Welcome to the VarDictJava wiki!

VarDict is a variant calling program designed to call SNP, MNP, indels up to 125 bp, as well as complex variants in next-generation sequencing in a single parse of BAM files.

VarDict performs local realignment on the fly and as a result, has unique capability calling long indels with accurate allele frequency estimation. It also handles complex variants with the combination of insertions and deletions, which actually quite common in the genome and missed by most variant callers.

Structural variants as INVersions, DUPlications, and DELetions also supported.