3616420
Somatic mutation detection
- Tools available
- SomaticSeq, Fang 2015
Nota:
- Incorporate the following five somatic mutation callers
- MuTect
Nota:
- 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
Nota:
- Good for high depth, up to 1e5. VarDict was the best indel detector when the VAF dipped below 50 %.
- SomaticSniper
- multiSNV
Nota:
- 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
Nota:
- http://www.biomedcentral.com/1471-2105/16/379 Good for deep sequencing over a small region.
- ShoRAH, V-Phaser 2, LoFreq, deepSNV, and RVD
Nota:
- Mostly devised for virus. Including QQSNV
- SomaticSeq, Fang 2015
- highlighted researches
- Considerations on the mutational rate of the LR PCR
- LR-PCR
- de novo assembly
Nota:
- 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
Nota:
- 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
- de novo assembly
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