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2_create_genetic_map_lepmap_SxG.Rmd

This file is part of "Genotypic data and genetic map for Syrah x Grenache bi-parental grapevine population".

Version 1.0
File Citation
Brault, Charlotte; Flutre, Timothée; Launay, Amandine; Doligez, Agnès; Chouiki, Hajar; Sarah, Gautier; Mournet, Pierre, 2021, "2_create_genetic_map_lepmap_SxG.Rmd", Genotypic data and genetic map for Syrah x Grenache bi-parental grapevine population, https://doi.org/10.15454/QEDX2V/V6SO6U, Portail Data INRAE, V1
Dataset Citation
Brault, Charlotte; Flutre, Timothée; Launay, Amandine; Doligez, Agnès; Chouiki, Hajar; Sarah, Gautier; Mournet, Pierre, 2021, "Genotypic data and genetic map for Syrah x Grenache bi-parental grapevine population", https://doi.org/10.15454/QEDX2V, Portail Data INRAE, V1, UNF:6:L5hd7gugVIod43JkBypJvQ== [fileUNF]
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doi:10.15454/QEDX2V/V6SO6U
1b16d9f9aa133a97200e37f0f8b32038
2021-05-25
32.1 KB
text/x-r-markdown
R and bash script that we used to produce the Syrah x Grenache consensus genetic map with Lep-MAP3 (Rastas et al., 2017), from the SNP data filtered by grouping with Carthagene. It takes as inputs the cleaned vcf file and the pedigree file produced with «create_files_for_lepmap.Rmd». Highly distorted and non-informative markers were removed (parameters removeNonInformative=1 and dataTolerance=0.001). Then markers were separated into 19 linkage groups with SeparateChromosome2 function, with a LOD threshold of 25 and a minimum marker number of 100. Singular markers were assigned to linkage groups with JoinSingles2All function. Markers assigned to wrong linkage groups according to their physical position were removed (7 markers). We applied the ordering function OrderMarkers2 5 or 10 times for each linkage group and kept the replicate with the largest likelihood. We performed a local polynomial regression (loess) of the genetic distance on the physical distance (span=0.8) to detect and remove markers with outlying genetic positions, e.g., markers far from others and not in the sigmoid shape (+/- 40 SE). These ordering and outlier detection steps were run 3 times (bash scripts "map_step1.sh", "map_step2.sh" and "map_step3.sh" given below). Duplicated markers with the same segregation were removed and a last ordering step was done (see bash script "map_step4.sh" given below) in order to produce the "SxG_GBS_lepmap_raw.map" (then, linkage group names need to be added in order to generate "SxG_GBS_lepmap.map") and "SxG_GBS_lepmap.loc" files with 3,964 markers. A "SxG_GBS.qua" file (given below) with a single fake phenotype was also produced for use in "3_analyse_map_quality.Rmd"
2020-10-15
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