TraceHaplotyper: using direct sequencing to determine the phase of an indel followed by biallelic SNPs.
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.
Seroussi
Yanir
Y
Technion-Israel Institute of Technology, Haifa, Israel. seroussi@agri.huji.ac.il
Seroussi
Eyal
E
D000465:Algorithms; D001483:Base Sequence; D005787:Gene Frequency / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics*; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D054643:INDEL Mutation; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011381:Programming Languages; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D005819:Genetic Markers