InDelGT: An integrated pipeline for extracting indel genotypes for genetic mapping in a hybrid population using next-generation sequencing data.

Premise: Although several software packages are available for genotyping insertion/deletion (indel) polymorphisms in genomes using next-generation sequencing data, simultaneously calling indel genotypes across many individuals for use in genetic mapping remains challenging.

Methods And Results: We present an integrated pipeline, InDelGT, for the extraction of indel genotypes from a segregating population such as backcross or F lines, or from an F cross between outbred species. The InDelGT algorithm is implemented in three steps: generating an indel catalog, calling indel genotypes, and analyzing indel segregation. We demonstrated the use of the pipeline with an example data set from an F hybrid population of and successfully constructed the two parental genetic linkage maps.

Conclusions: InDelGT is a practical tool that can quickly genotype a large number of indel markers within a population following Mendelian segregation. The InDelGT pipeline is freely available on GitHub (https://github.com/tongchf/InDelGT).