Mutascope

[…] ative allele or an artifact []. Advances in the bioinformatics field led to the creation and the development of algorithms to manage such artifacts during the analysis (e.g.: AmpliVar [], TSSV [] and Mutascope []). AmpliVar is based on the reduction of the number of input reads to be aligned to a reference genome by grouping for primer sequence in a key-value structure, where each group is analyze […]

[…] ced them using Illumina MiSeq sequencer for 2x150 bp reads. The sequencing reads were then aligned and mutation called using the Illumina BaseSpace cloud with TruSeq DNA amplicon application or using Mutascope locally []. To increase the detection sensitivity the reads spanning the expected 42 nt deletion in AA2476T tumor were aligned independently using BLAT []. To analyze the large deletion in s […]

[…] ple (Celemics, Seoul, Korea). Subsequently, each product was indexed, mixed, and deeply sequenced on HiSeq2500. Raw data was deindexed and mapped to the reference human genome (hg19) using NovoAlign. Mutascope was used to call somatic mutations, and compared to the whole exome sequencing data []. Only the loci with at least 500 reads of both normal and tumor tissue and >5% allelic fraction were us […]

[…] s at genome scale. Existing algorithms for identifying pSNMs from whole-genome or targeted resequencing data require a matched control sample, such as JointSNVMix, Varscan 2, Strelka, EBCall, muTect, Mutascope, and LoFreq. As a result, fundamental patterns of the pSNMs in whole genomes of clinically unremarkable individuals remain largely unknown, such as the prevalence, allele fractions, mutation […]