Overview

This section describes each step of the RABBIT pipeline, illustrated by a simulated connected multiparental population. See pipeline.jl for the collection of julia code blocks on this page. See pipeline.cmd for window CMD or pipeline.sh for Unix/Linux shell. See "RABBITDocs\docs\src\pipeline" for all the scripts and output files.

S1 MagicSimulate
S2 MagicFilter
S3 MagicCall
S4 MagicMap
S5 MagicImpute
S6 MagicReconstruct
S7 MagicScan

Pipeline

Skip MagicCall and MagicMap if a reliable markermap (physical or genetic) is available.
Perform MagicCall for sequence data in heterozygous mapping populations.

Code for CLI

Code blocks for CLI start with julia rabbit_funcname.jl, assuming that the paths to julia.exe and the main function file have been added in the platform environmental variable PATH. See section "Guide/Run julia in CLI".