Ylaine/2009-7-13
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False Negatives[edit]
- Continue debugging code from Friday
- Split SNP file into 4 1M-line files; 48759 in target region
- Search for locations in 'noseven.chrlocs' using 'grep' within 'system'
my $command = "grep 'chr$chr\t$loc' $locsfile"; system($command);
- MAQ/MAQ default SNP calling returned 8376 SNPs, 5906 of which have coverage >= 8x
- Use 'grep' -f to search for locs in MAQ results:
grep -c -f covered.targetSNPsaa ../testout.txt
- Found 6503 SNPs in 8x covered region. 4275 also found by MAQ (false negative rate of 34.26%)
BWA/SAM[edit]
- Compare results using default filter and filter written by Dr. Zhang to results obtained with MAQ
- Files are:
NA12878_40bp_061109.sequence.pileup.varFilter.txt NA12878_40bp_061109.sequence.pileup.variants.txt
- 9077/14996 of SNPs in 'variants' at dbSNP locations
- 1K Genome comparison: (edited 7/15/09)
1K Genome | In dbSNP | Percent | Not in dbSNP | Percent |
Match | 7836 | 86.33% | 222 | 3.75% |
Miss | 752 | 8.28% | 5662 | 95.66% |
Mismatch | 489 | 5.39% | 35 | 0.59% |
Total | 9077 | 5919 | ||
- Using method from Friday, FP rate is 34.49%
- Average quality comparison (not sure what the columns are):
' | Col 5 | Col 6 | Col 7 | Col 8 |
In dbSNP | 74.25 | 81.56 | 36.04 | 12.41 |
s.d. | 54.59 | 58.25 | 3.01 | 11.58 |
Not in dbSNP | 39.30 | 40.64 | 34.50 | 10.79 |
s.d. | 26.06 | 27.77 | 4.58 | 10.12 |
- According to website, columns should be consensus quality, SNP quality, maximum mapping quality, and read number (coverage)
http://samtools.sourceforge.net/cns0.shtml