Revision as of 22:38, 15 July 2009 by >Ylaine
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