Ylaine/2009-8-18
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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]
- Worked on snpInArm.pl
../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 | ||
ROC[edit]
- Summary table:
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% |