Ylaine/2009-7-9

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Revision as of 18:55, 9 July 2009 by >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...)
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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

' In dbSNP Not in dbSNP
Homozygous: 0.553341467 0.207207207
Heterozygous: 0.446658533 0.792792793
Transition: 0.764795144 0.671717172
Transversion: 0.235204856 0.328282828
Total: 7377 999