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GATK / Genome Analysis ToolKit
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Focuses on variant discovery and genotyping. GATK provides a toolkit, developed at the Broad Institute, composed of several tools and ables to support projects of any size. The application compiles an assortment of command line allowing one to analyze of high-throughput sequencing (HTS) data in various formats such as SAM, BAM, CRAM or VCF. The website includes multiple documentation for guiding users.
Lacer
Recalibrates base quality scores without assuming knowledge of correct and incorrect bases and without requiring knowledge of common variants. Lacer is an accurate base recalibrator. It enhances variant identification accuracy for resequencing data of human like organisms which improve and extend the benefits of base quality score. Lacer uses an algorithm which directly extracts quality scores and aggregate error probabilities based on the assumption that correct and incorrect bases have different quality score profiles.
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