Ylaine/2009-8-18: Difference between revisions
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>Ylaine |
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* Which of these are covered by other probes? | * Which of these are covered by other probes? | ||
../Scripts/snpTargeted.pl snp.arms.1k >arms.target & | ../Scripts/snpTargeted.pl snp.arms.1k >arms.target & | ||
../Scripts/threshold.pl arms.target 8 >cov8.arms | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''Targeted''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''Only arms''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''Targeted (8x)''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''Only arms (8x)''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
|- | |||
| 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|| | |||
|- | |||
| | |||
|} |
Revision as of 23:19, 18 August 2009
Finding Targeted SNPs
- 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
' | 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
- 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 | ||||