TraceHaplotyper: using direct sequencing to determine the phase of an indel followed by biallelic SNPs

Biotechniques. 2007 Oct;43(4):452, 454, 456. doi: 10.2144/000112552.

Abstract

Sequencing of a diploid PCR product that is heterozygous for an indel mutation and a downstream single nucleotide polymorphism (SNP) allows determination of haplotype phase. Manual determination of phase from trace files of this type is tedious; therefore, we introduce the Perl script TraceHaplotyper, which works from the expected sequence to analyze a sequencing trace file for the sites that are informative for the genotyping and outputs the two underlying haplotypes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Base Sequence
  • Gene Frequency / genetics
  • Genetic Markers / genetics*
  • Genotype
  • Haplotypes / genetics*
  • INDEL Mutation*
  • Molecular Sequence Data
  • Polymorphism, Single Nucleotide / genetics*
  • Programming Languages
  • Sequence Analysis, DNA / methods*
  • Software*

Substances

  • Genetic Markers