LOHGIC

LOHGIC infers mutational status using AIC weights (W). Khiabanian et al. 2017.
LOH-Germline Inference Calculator (LOHGIC) detemines mutational status of variants identified in deep-sequencing assays. It also predicts loss of heterozygosity (LOH) and provides additional information on the number of mutated alleles in tumor cells based on specimen’s purity and a variant’s allele frequency, sequencing depth, and ploidy. Statistical uncertainties inherent to these parametrs are also considred. (When ploidy is set at two, LOH with the loss of wild-type copy is also considered.)

  MERIT

MERIT precisely quantifies ultra-deep sequencing error. Hadigol and Khiabanian 2017.
Mutation Error Rare Identification Toolkit (MERIT) is a comprehensive pipeline designed for in-depth quantification of erroneous substitutions and small indels in high-throughput sequencing data, specifically, for ultra-deep applications. MERIT considers the genomic context of the errors, including the nucleotides immediately at their 5’ and 3’, and establishes error rates at 96 possible substitutions as well as four single-base and 16 double-base indels.


© Khiabanian Lab 2015

Rutgers University
Rutgers Cancer Institute
Center for Systems and Computational Biology
Department of Pathology and Laboratory Medicine


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