Ylaine/2009-8-6

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Error Classification[edit]

  • Write script to tag SNP mismatches from gold standard set as type I or II errors: 'fnErrorType.pl'
../Scripts/fnErrorType.pl fn.1K snp.chr.txt>fn.1K.errors
    • Only 87/2910 errors are type 1 at coverage >1 (found 2898 errors on 7/29??)
  • Write script to return SNPs above coverage threshold, 'threshold.pl'
../Scripts/threshold.pl fn.1K.errors 8 > fn.8.temp
' Type 1 Type 2 Total
2x 87 2823 2910
8x 23 221 244
10x 21 137 158
20x 8 27 35
  • Alternatively:
' Type 1 Type 2
2x 2.99% 97.01%
8x 9.43% 90.57%
10x 13.29% 86.71%
20x 22.86% 77.14%

File:Fn errortype.jpg

False Positives[edit]

  • Effect of probe efficiency
/Users/kunzhang/WorkSpace/Exome/Solexa/NA12878/Exome_Probe_efficiency.txt
    • Use grep to categorize efficiency into 6 bins:
~/NA12878/Probes
Bin # Efficiency Number
1 [1,20] 138835
2 [21,40] 27059
3 [41,60] 9714
4 [61,80] 4027
5 [81,100] 1813
6 >100 1247
  • Writing 'calculateSNPeff.pl'
    • Assume ranges are inclusive of region strictly between target arms