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===Part 5=== "Using 1KG data as reference, what is our false positive rate as the function of the filter we used? This could be plotted as a curve. Also what is the total variants we can call as the function of false-positive rate?" * Compare to 1KG data ../Scripts/compare1K.pl orig.snp>snp.1k * Separate into matches and misses. There are 74 heterozygous and 522 homozygous mismatches grep 'match' snp.1k |grep 'het'>1k.match.het.txt grep 'match' snp.1k |grep 'homo'>1k.match.homo.txt grep 'miss' snp.1k |grep 'homo'>1k.miss.homo.txt grep 'miss' snp.1k |grep 'het'>1k.miss.het.txt ** EDIT 8/18: mismatches put into match file *Use [pPresent, numPresent] output of Matlab script 'snpCurve.m' * False positive rate as function of filter: [[Image:Aug17_percent1k.jpgβ]] ** Lower left hand corner: [[Image:Aug17 percent1k closeup.jpg]] * ROC (each "stripe" is either a single quality or coverage threshold) [[Image:Aug17_roc.jpg]] [[Image:Aug17_roc2.jpg]]
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