SMUG (Somatic Mutation Gleaner) was developed to effectively detect base substitutions and loss of heterozygosity (LOH) using next-generation sequencing data for normal and tumor tissues. It first screens bam files using walker programs (modules we developed to run under GATK), and then summarizes the results using Perl scripts.
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Song Z, Long J, He J, Shi J, Shu XO, Cai Q, Zheng W, Li C (2012)
Efficient detection of tumor somatic mutations using next-generation sequencing data.
(to be submitted)