From: Next generation sequencing in cancer research and clinical application
Category | Program | URL | Ref |
---|---|---|---|
Alignment | MAQ | [34] | |
BWA | |||
Bowtie2 | [37] | ||
BFAST | [38] | ||
SOAP2 | [39] | ||
Novoalign/NovoalignCS | Â | ||
SSAHA2 | [40] | ||
SHRiMP | [41] | ||
Mutation calling | GATK | [42] | |
Samtools | [43] | ||
SOAPsnp | [44] | ||
SNVmix | [45] | ||
VarScan | |||
Somaticsniper | [51] | ||
JointSNVMix | [52] | ||
SV detection | BreakDancer | [57] | |
VariationHunter | [58] | ||
PEMer | [59] | ||
SVDetect | [60] | ||
Function effect of mutation | SIFT | [53] | |
CHASM | [55] | ||
PolyPhen-2 | [54] | ||
ANNOVAR | [56] |