Search Results for "somatic" - Page 2

LoDel is a Java based somatic deletion caller designed for whole-genome sequencing data from unmatched samples. LoDel is specialized for identifying somatic deletions with frequently existing sampling issues : low mutational frequency in cell population and absence of the matched control samples. The important features of LoDel are: •Estimation of accurate mutation frequency in a mixed disease sample •Improved somatic deletion calling based on the probabilistic model with the parameter estimation

...The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM) data to robustly estimate the conditional probability of segregation in a family, as well as the probability of it being de novo or somatic. In familial cases, various modes of inheritance are considered: X-linked, autosomal dominant, and recessive (homozygosity or compound heterozygosity). Moreover, VariantMaster integrates phenotypes and genotypes, and employs Annovar to produce additional information as allelic frequencies in general population and damaging scores.

Cake, a bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. Cake can be run on a high-performance computer cluster or used as a stand-alone application For additional information on how to obtain and run Cake, updates and known issues please visit the wiki page https://sourceforge.net/p/cakesomatic/wiki/Cake%20Somatic/

THIS IS NO LONGER THE HOME FOR SEURAT. PLEASE GO TO https://sites.google.com/site/seuratsomatic/ --- Seurat is an sequence analysis program for somatic mutation and allelic imbalance discovery in paired tumor and normal genome and transcriptome data.