Ylaine/2009-8-18: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Ylaine
>Ylaine
Line 9: Line 9:
** 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