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{{ AGLabEntry|2009-8-19|2009-8-21 }} =False Positive SNPs= * 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= * 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
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