Rcross input files Up: Data files Previous: Data files Contents Index MAPMAKER raw files. Rcross will convert Mapmaker/QTL raw files for use in the QTL Cartographer system. You will first need to use Mapmaker/EXP to create a genetic linkage map. Then convert the map into the ``Rmap.out'' format for use with Rmap.Then, use Rcross to convert the Mapmaker/QTL raw data file into the ``Rcross.out The marker format is identical and there are no issues with incorrectly coded SNP calls. The input data does not include phase information, but this has not been an issue with the other read.cross can read some JoinMap/MapQTL files, format="mapqtl". Here are the details from the help for read.cross: MapQTL format. This format requires three files, described in the manual of the MapQTL program (same as JoinMap). genfile corresponds to the loc file containing the genotype data. Each marker and its genotypes should be on a single Lep-MAP3 (LM3) is a novel linkage map construction software suite. It can handle millions of markers and thousands of 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. However, as the input data should be given as VCF. The VCF data format was developed for the 1000 Genomes Project by the International 1000 Genomes Consortium. For further informations please access the 1000 Genome Project webpage where not only are included several new populations, but also included the populations of the HapMap Project. This guide was based upon the wiki of 1000 Genomes Project . I'm at question 4 now (converting genotype codes) but can't properly relate your explanation to the JoinMap/MapQTL manual for cases 5 to 14, sorry. MapQTL considers 5 segregation types (table 6 in the manual):: locus heterozygous in both parents, four alleles (no dominance allowed) This is close to the Kosambi distance of the consensus map (2891 cM) when the distance is calculated using the Haldane to Kosambi equation provided in the JoinMap manual. Additionally, the correlation between number of markers per map and total map length was r = 0.874, p < 0.01. These investigations support (1) the idea that the large number