Somatic mutation detection

Somatic mutation detection

1. Tools available

   • SomaticSeq, Fang 2015
     • Incorporate the following five somatic mutation callers
   • MuTect
     • MuTect performed the best when the normal contained no tumor contamination (see Additional file 1: Tables S2 and S3). It was by far the most sensitive tool among those we have tested when the normal was pure and tumor VAF was very low.     
   • JointSNVMix2
   • VarScan2
   • VarDict
     • Good for high depth, up to 1e5. VarDict was the best indel detector when the VAF dipped below 50 %. 
   • SomaticSniper
   • multiSNV
     • takes multiple tumor sam- ples from the same patients to take advantage of evo- lution modeling in heterogeneous cancers to increase the sensitivity and specificity of somatic mutation detec- tion
   • QQSNV
     • http://www.biomedcentral.com/1471-2105/16/379 Good for deep sequencing over a small region.
   • ShoRAH, V-Phaser 2, LoFreq, deepSNV, and RVD
     • Mostly devised for virus. Including QQSNV

2. highlighted researches

3. Considerations on the mutational rate of the LR PCR

4. LR-PCR

   • de novo assembly
     • Doesn't work atm. might need to extract seqs aligned to ABCA4 first before de novo
   • Mutations on promoters/splice site/histone markers
   • Use Exom sequencing result to estimate polymerase error-rate
     • Not necessary, since the error rate is supposed to be limited, given the DNA sample's good quality
   • Use CADD / VAAS2 to re-predict deleterious mutations