Athurva Gore/LabNotes/2009-8-20

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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