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

Yanir Seroussi | Zendy; Eyal Seroussi | Zendy

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

Author(s) -

Yanir Seroussi,

Eyal Seroussi

Publication year - 2007

Publication title -

biotechniques

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.617

H-Index - 131

eISSN - 1940-9818

pISSN - 0736-6205

DOI - 10.2144/000112552

Subject(s) - indel , genetics , biology , haplotype , genotyping , single nucleotide polymorphism , perl , snp genotyping , snp , indel mutation , dna sequencing , computational biology , genotype , gene , computer science , world wide web

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.

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