Ylaine/2009-8-10
Jump to navigation
Jump to search
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