Ylaine/2009-8-10: Difference between revisions
Jump to navigation
Jump to search
>Ylaine (New page: ==Heterozygous SNP filtering== * debug probe efficiency script * Turns out probes file is not correct - should be 3x as many probes. File updated. {| {{table}} | align="center" style="back...) |
>Ylaine |
||
Line 16: | Line 16: | ||
|- | |- | ||
| 5||>10000||33 | | 5||>10000||33 | ||
|- | |||
| | |||
|} | |||
~/NA12878/Scripts/calculateSNPeff.pl hiqual>hiqual.eff & | |||
grep 'het' hiqual.eff | grep 'rs' > hiqual.het_in.txt | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''Min. Probe #''' | |||
| align="center" style="background:#f0f0f0;"|'''Total''' | |||
| align="center" style="background:#f0f0f0;"|'''In dbSNP''' | |||
| align="center" style="background:#f0f0f0;"|'''(percent)''' | |||
|- | |||
| 0||5237||4638||88.56% | |||
|- | |||
| 1||5100||4544||89.10% | |||
|- | |||
| 2||1568||1427||91.01% | |||
|- | |- | ||
| | | | ||
|} | |} | ||
* try using allele counts to identify false positives | * try using allele counts to identify false positives |
Latest revision as of 00:33, 11 August 2009
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