Revision as of 17:18, 19 August 2009 by >Ylaine
Finding Targeted SNPs[edit]
- New script, snpTargeted.pl adapted from snpInRange.pl
../Scripts/snpTargeted.pl orig.snp>snp.targeted&
- Got 17557/20761 or 84.57%
- Follow-up questions:
- Is there a bug in calculateSNPeff.pl?
- What proportion of targeted SNPs are matches?
- How many SNPs are present in target arms?
- Are (heterozygous) mismatches more likely to occur in non-targeted regions?
- What is the median coverage of targeted regions vs. non-targeted regions?
Comparing to 1KG[edit]
'
|
All
|
'
|
Targeted
|
'
|
Match |
16319 |
78.60% |
15579 |
88.73%
|
Mismatch |
596 |
2.87% |
392 |
2.23%
|
Miss |
3846 |
18.53% |
1586 |
9.03%
|
|
- More matches among targeted SNPs
- Threshold coverage:
../Scripts/threshold.pl snp.targeted.1k 8 > cov8.target
../Scripts/threshold.pl snp.1k 8 > cov8.all
'
|
All
|
'
|
Targeted
|
'
|
Match |
13548 |
92.11% |
13274 |
92.78%
|
Mismatch |
125 |
0.85% |
111 |
0.78%
|
Miss |
1035 |
7.04% |
922 |
6.44%
|
Total |
14708 |
|
14307 |
|
|
- CONCLUSION: if SNPs are thresholded at 8x coverage, the additional exclusion of off-target SNPs does not significantly decrease the false positive rate.
SNPs in Arms[edit]
../Scripts/snpInArm.pl orig.snp > snp.arms
../Scripts/compare1K.pl snp.arms>snp.arms.1k
'
|
Arms
|
'
|
Arms >=8x
|
'
|
Match |
469 |
64.16% |
409 |
82.96%
|
Mismatch |
20 |
2.74% |
12 |
2.43%
|
Miss |
242 |
33.11% |
72 |
14.60%
|
Total |
731 |
|
493 |
|
|
- Which of these are covered by other probes?
../Scripts/snpTargeted.pl snp.arms.1k >arms.target &
../Scripts/threshold.pl arms.target 8 >cov8.arms
'
|
Targeted
|
'
|
Only arms
|
'
|
Targeted (8x)
|
'
|
Only arms (8x)
|
'
|
Match |
458 |
79.51% |
11 |
7.10% |
405 |
82.15% |
4 |
20.00%
|
Mismatch |
19 |
3.30% |
1 |
0.65% |
11 |
2.23% |
1 |
5.00%
|
Miss |
99 |
17.19% |
143 |
92.26% |
57 |
11.56% |
15 |
75.00%
|
Total |
576 |
|
155 |
|
493 |
|
20 |
|
|
- But what about SNPs that are targeted but aren't in arms?
../Scripts/snpInArm.pl snp.targeted.1k > snp.targeted.arms &
'
|
No Arms
|
'
|
>=8x
|
'
|
Match |
15120 |
89.05% |
12868 |
93.02%
|
Mismatch |
373 |
2.20% |
100 |
0.72%
|
Miss |
1487 |
8.76% |
865 |
6.25%
|
Total |
16980 |
|
13833 |
|
|
Filter
|
# of SNPs
|
Miss
|
Mismatches
|
Total Errors
|
None |
20761 |
18.53% |
2.87% |
21.40%
|
>=8x coverage |
14708 |
7.04% |
0.85% |
7.89%
|
Targeted |
17557 |
9.03% |
2.23% |
11.27%
|
Targeted (8x) |
14307 |
6.44% |
0.78% |
7.22%
|
Targeted, no arms |
16980 |
8.76% |
2.20% |
10.95%
|
Targeted, no arms (8x) |
13833 |
6.25% |
0.72% |
6.98%
|
|