Package 

Class PurgeSequencesFromAlignments

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description

    • Constructor Summary

      Constructors 
      Constructor Description

    • Enum Constant Summary

      Enum Constants 
      Enum Constant Description

    • Method Summary

      Modifier and Type Method Description
      static void main(Array<String> args)
      static Optional<GenotypeTable> filterBadAlignments(GenotypeTable genotypeTable, double maxDist, int minSiteCount, double minMAF) This method eliminates high distances alignments after all GAPs have been converted to N, and then it filters on coverage and minimum MAF

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

    • Method Detail

      • filterBadAlignments

         static Optional<GenotypeTable> filterBadAlignments(GenotypeTable genotypeTable, double maxDist, int minSiteCount, double minMAF)

        This method eliminates high distances alignments after all GAPs have been converted to N, and then it filters on coverage and minimum MAF