PureCN: copy number calling and SNV classification using targeted short read sequencing
...loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clona...C, Chiang D, Morrissey M (2016). “PureCN: Copy number calling and SNV classification using targeted...2105 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...not needed Output: LoFreq Description: SNV caller, Python language, stan...l Output: VCF MarginAlign Description: SNV caller, specifically tailored...nnotation Dependent Depletion; tool for scoring SNV deletions/insertions; “...2918 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
...nbsp;k-mers profiles of the RNA-seq paired-end reads Software (Java) https://github.com/ChimeRScope/ChimeRScope/wiki FastGT Genotyping of known SNV/SNP variants directly from ra...2380 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number...Tags: PureCN, copy, number, calling, SNV, classification, targeted, short, read, sequencing
2105 days ago
List of non-commercial NGS genotype-calling software
Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated w...Tags: List, non-commercial, NGS, genotype-calling, software, tools, snv
2105 days ago