Ylaine/2009-7-9
Jump to navigation
Jump to search
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 |