Ylaine/2009-8-18: Difference between revisions

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>Ylaine
>Ylaine
Line 3: Line 3:
  ../Scripts/snpTargeted.pl orig.snp>snp.targeted&
  ../Scripts/snpTargeted.pl orig.snp>snp.targeted&
* Got 17557/20761 or '''84.57%'''
* 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?

Revision as of 18:48, 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?