Ylaine/2009-7-9: Difference between revisions

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>Ylaine
(New page: ==SNP Filtering== * Wrote 'extractSNPlines.pl' to get pileup lines by line number (instead of grep-ing for position) ./extractSNPlines.pl notwo.pileup snoOrigLocs.txt > snp.pileup * Disco...)
 
>Ylaine
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==Yesterday's SNP Frequency Measurements==
==Yesterday's SNP Frequency Measurements==
* Possible over-representation of heterozygous SNPs: much more common among presumed false positives than direct hits.
{| {{table}}
{| {{table}}
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|''''''
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| align="center" style="background:#f0f0f0;"|'''Not in dbSNP'''
| align="center" style="background:#f0f0f0;"|'''Not in dbSNP'''
|-
|-
| Homozygous:||0.553341467||0.207207207
| Homozygous:||55.33%||20.72%
|-
|-
| Heterozygous:||0.446658533||0.792792793
| Heterozygous:||44.67%||79.28%
|-
|-
| Transition:||0.764795144||0.671717172
| Transition:||76.48%||67.17%
|-
|-
| Transversion:||0.235204856||0.328282828
| Transversion:||23.52%||32.83%
|-
|-
| Total:||7377||999
| Total:||7377||999

Revision as of 18:57, 9 July 2009

SNP Filtering

  • Wrote 'extractSNPlines.pl' to get pileup lines by line number (instead of grep-ing for position)
./extractSNPlines.pl notwo.pileup snoOrigLocs.txt > snp.pileup
  • Discovered that pileup does not output SNP calls. Modify 'heterozygousSNPfilter.pl' to extract heterozygous SNPs 'cns.final.snp', put call into hash keyed by position. Then iterate through lines of snp.pileup and count occurrences of each called nucleotide.

Yesterday's SNP Frequency Measurements

  • Possible over-representation of heterozygous SNPs: much more common among presumed false positives than direct hits.
' In dbSNP Not in dbSNP
Homozygous: 55.33% 20.72%
Heterozygous: 44.67% 79.28%
Transition: 76.48% 67.17%
Transversion: 23.52% 32.83%
Total: 7377 999