Lep-MAP2 Wiki

Linkage map construction suite

Brought to you by: fedster9, lep-map, mattb23

Home

Authors:

Lep-MAP2 : Documentation

Lep-MAP2 (LM2) is a novel linkage map construction software suite. It can handle tens of thousands of markers and individuals possibly on multiple families. Input genotype data can be from genome sequencing (RADseq or whole genome sequencing), SNP assay, microsatellites or any mixture of them.

The following wiki will document its features. Each module of LM2 is documented in [Modules] with examples on simulated data. The used data can download here. Also some useful scripts can be downloaded here.

Installation

LM2 is implemented in java. To run it, java runtime environment is required, see eg. java.com. To compile it, java development kit is required.

The compiled classes and source code of Lep-MAP2 can downloaded from (this) sourceforge page (as a zip or from git). The code is available under GNU public license.

[Modules]

Useful scripts

linkage2post.awk, simpleconvert.awk : these are used to convert linkage files to posteriors and back, needed to run ParentCall (to impute missing parental genotypes or to call markers in the sex chromosome)

loc2linkage : this will convert JoinMap files to linkage files

vcf2posterior.awk : this will convert vcf files to Lep-MAP posteriors (takes PL field from a vcf). The pedigree information must be added separately.

Note: script transpose_tab can become very slow with many markers. Now there is the Transpose module in Lep-MAP that does transposes faster (replace "./transpose_tab" with "java [-cp bin] Tranpose").