Athurva Gore/LabNotes/2009-8-20
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[edit]
False Positive SNPs[edit]
- Currently checking to see if clonal reads could be influencing false positive SNPs.
- Added a step to variant caller that removes clonal reads (rmdup)
- Testing on HL003_merged "high false positive" set.
- Removing clonal reads does not have any effect; downsampling seems to remove them in a similar way
- No advantage gained.
- MAQ, however, does something more interesting
- MAQ only calls 2500 SNPs from HL003 NA12878 set.
- Most of them are at dbSNP locations (only 300 not)
- MAQ is being much more conservative somehow
- Taking into account mapping quality? What about taking into account neighboring consensus quality?
Probe Design[edit]
- Need to redesign two sets:
- TDMR Set
- CpG-SNP Set
- Both should have H1+Target+H2 constrained to 105
- Also, adjust P2MIP script to have a maximum combined arm size of 45.
- Allows sequencing without library construction