Ylaine/2009-8-10: Difference between revisions

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>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
 
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| 5||>10000||33
| 5||>10000||33
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~/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)'''
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| 0||5237||4638||88.56%
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| 1||5100||4544||89.10%
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| 2||1568||1427||91.01%
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|}
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* 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