Ylaine/2009-8-10

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Heterozygous SNP filtering[edit]

  • debug probe efficiency script
  • Turns out probes file is not correct - should be 3x as many probes. File updated.
Bin Max Eff. Size
1 1 128741
2 10 80195
3 100 106787
4 1000 2882
5 >10000 33
~/NA12878/Scripts/calculateSNPeff.pl hiqual>hiqual.eff &
grep 'het' hiqual.eff | grep 'rs' > hiqual.het_in.txt
Min. Probe # Total In dbSNP (percent)
0 5237 4638 88.56%
1 5100 4544 89.10%
2 1568 1427 91.01%
  • try using allele counts to identify false positives