SNV分析软件/工具

体细胞SNV Calling 的文献：
A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
网址：https://www.sciencedirect.com/science/article/pii/S2001037017300946#bb0120

GATK、samtools、bcftools、Varscan、Freebayes、Platypus、SNVer

TASSEL-GBS：高容量基因分型序列分析流程
SNVMix：检测单碱基突变
DeepVariant：机器学习
JointVMix(JSM)：检测正常/肿瘤配对NGS数据中体细胞突变的概率模型
Avocado：variant caller程序
NGSEP：集成框架
Reveel：SNV calling and 大群组genotyping
Atlas2：变异分析工具，Ruby语言
LoFreq：超敏感variant caller程序，perl语言
SNVSniffer： Germline and Somatic SNV and indel
Strelka：small variant caller，分析小群组中的种系变异和肿瘤/正常样本对中的体细胞变异
SomaticSniper：鉴定肿瘤与正常之间不同的单核苷酸位置
Breseq：来预测样本中相对于已经测序的基因组的突变
FaSD: Somatic SNV detection program
CASAVA ： filter FASTQ files
Mutect ：GATK的命令

somatic SNV工具网站：https://omictools.com/somatic-snp-detection-category

部分工具网址：

BAYSIC https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-104
CAKE https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740632/
deepSNV https://academic.oup.com/bioinformatics/article/30/9/1198/234115
EBCall https://academic.oup.com/nar/article/41/7/e89/1073733
Indelocator https://software.broadinstitute.org/cancer/cga/indelocator
Isaac variant caller https://academic.oup.com/bioinformatics/article/29/16/2041/199472
JointSNVMix https://academic.oup.com/bioinformatics/article/28/7/907/209164
LoFreq https://academic.oup.com/nar/article/40/22/11189/1152727
MutationSeq https://academic.oup.com/bioinformatics/article/28/2/167/197256
Mutect
Pindel
QuadGT http://www.iro.umontreal.ca/~csuros/quadgt/
samtools mpileup
Seurat https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-302
Shimmer https://academic.oup.com/bioinformatics/article/29/12/1498/292411
SolSNP https://sourceforge.net/projects/solsnp/
SNVMix https://academic.oup.com/bioinformatics/article/26/6/730/245170
SOAPsnv
SomaticCall
SomaticSniper https://academic.oup.com/bioinformatics/article/28/3/311/188933
Strelka https://academic.oup.com/bioinformatics/article/28/14/1811/218573
VarDict
VarScan2 https://genome.cshlp.org/content/22/3/568.long
Virmid https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-8-r90
CancerMutationAnalysis https://bioconductor.org/packages/release/bioc/html/CancerMutationAnalysis.html
NextGENe https://softgenetics.com/NextGENe_014.php
RADIA https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111516
Shimmer https://academic.oup.com/bioinformatics/article/29/12/1498/292411
qSNP http://www.doc88.com/p-1106634164566.html