Ylaine/2009-8-18: Difference between revisions
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** Are (heterozygous) mismatches more likely to occur in non-targeted regions? | ** Are (heterozygous) mismatches more likely to occur in non-targeted regions? | ||
** What is the median coverage of targeted regions vs. non-targeted regions? | ** What is the median coverage of targeted regions vs. non-targeted regions? | ||
===Comparing to 1KG=== | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''All''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''Targeted''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
|- | |||
| 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 |
Revision as of 20:34, 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