Revision as of 00:33, 11 August 2009 by >Ylaine
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