Class TsTvStats

java.lang.Object
org.snpeff.stats.TsTvStats
All Implemented Interfaces:
SamplingStats<VcfEntry>

public class TsTvStats extends Object implements SamplingStats<VcfEntry>
Calculate Ts/Tv rations per sample (transitions vs transversions)
Author:
pablocingolani
  • Constructor Details

    • TsTvStats

      public TsTvStats()
  • Method Details

    • getTransitions

      public long getTransitions()
    • getTransversions

      public long getTransversions()
    • getTsTvRatio

      public double getTsTvRatio()
      Transitions / transverions ratio WARNING: I removed the '2.0' factor because it mostly confused people. I clarify that the ratio is a 'raw' ratio in the summary page ------------------------------------------------------------------------ Comments that follow are out-dated. I leave it here just for reference. Note: Why is there a '2' in the ratio and not just "number of transitions / number of transverions"? From Casey Bergman (Manchester Univ.) Ts:Tv ratio is a ratio of rates, not observed events. Imagine observing 100 sites with transitions and 100 sites with transversions. Your method would say that the Ts:Tv rate ratio is 1. But since there are 4 possible Tv mutation types and only 2 possible Ts mutation types, in this example there is actually a 2-fold higher rate of Ts mutations that Tv mutations per site. Thus, the Ts:Tv (rate) ratio is 2:1 References: http://www.mun.ca/biology/scarr/Transitions_vs_Transversions.html http://biostar.stackexchange.com/questions/4759/ti-tv-ratio-confirms-snp-discovery-is-this-a-general-rule/
      Returns:
    • hasData

      public boolean hasData()
      Does this stat have any data
      Specified by:
      hasData in interface SamplingStats<VcfEntry>
      Returns:
    • isTransition

      public boolean isTransition(String ref, String alt)
      Is this a transition?
      Parameters:
      ref - : Reference base (upper case)
      alt - : Alternative base (upper case)
      Returns:
    • isTranversion

      public boolean isTranversion(String ref, String alt)
      Is this a transversion?
      Parameters:
      ref - : Reference base (upper case)
      alt - : Alternative base (upper case)
      Returns:
    • sample

      public void sample(VcfEntry vcfEntry)
      Update Ts and Tv counters Only for SNPs
      Specified by:
      sample in interface SamplingStats<VcfEntry>
    • toString

      public String toString()
      Show results to stdout
      Overrides:
      toString in class Object