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=NA12878 High False Positive Reads= * Locations ** 07282009_HL002, Lanes 4-7 ** 08052009_HL003, Lanes 4-5 * Storing data on genome-miner:/media/TmpStore1/AG_Scratch/Exome/NA12878 * Using this sample for validation ** First step, need to map these reads. ** Start out with reads on a per experiment basis *** Merge s_4 through s_7 in HL002, merge s_4 and s_5 in HL003 *** Run Bowtie-SAM script on these merged sets; check results *** Bowtie-SAM has been run on both HL003 and HL002. * HL002 has a TON of SNPs. ** 185k! ** Something is very odd here. * Noticed that HL002 and one set from HL003 both used size-selection. ** Not sure about Billy's results * Looked for a homozygous overrepresentation. ** In HL002, definite presence of homozygous SNPs over heterozygous SNPs. * Next Steps: ** Check both of these samples against dbSNP ** Check both of these samples against 1KG ** Is there anything similar among the false positives?
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