Data from: RAD-sequencing for estimating GRM-based heritability in the wild: a case study in roe deer

*NCBI BioProject PRJNA533008: Provide all FASTQ data already demultiplexed and preprocessed.*sensitivity_analysis.R: R script with explanations to run sensisitivity analysis using ASREML-R v3.00*phenotype.csv: A csv file containing individual phenotypic informations. ANIMAL is the name of the individuals. BODYMASS is their bodymass in kg. AGE and SEX correspond to class-age and sex of individuals respectively.*grm_uniq_hwe0.05_maxmissXX_mafXX.grm: Genomic Relatedness Matrix built from the SNPs called using the S3 'Intermediate' set of parameters.*full_indiv_barcorde.txt(not necessary for denovo_map.pl): A file with describing individuals in 4 columns.*population.map: A file containing two columns with assignments of each of the samples to a particular population.*stacksoutput_maxloc.vcf: Output file of *populations* program of Stacks software, run using the S1 MaxLoci set of parameters: -m=2 -M=2 -N=4 --max_locus_stacks=5 -n=1*stacksoutput_minerr.vcf: Output file of *populations* program of Stacks software, run using the S2 MinError set of parameters: -m=11 -M=2 -N=4 --max_locus_stacks=5 -n=1*stacksoutput_default.vcf: Output file of *populations* program of Stacks software, run using the S4 Default set of parameters: -m=3 -M=2 -N=4 --max_locus_stacks=3 -n=1*stacksoutput_intermediate.vcf: Output file of *populations* program of Stacks software, run using the S3 Intermediate set of parameters: -m=7 -M=2 -N=4 --max_locus_stacks=5 -n=1*indiv_to_rm.txt: Empty text file to fill with individual names needed to be remove for future analysis(e.g. individuals with too many missing data, replicatesamples).*script_QCfiltering.sh: A shell script with explanations to run the different quality filtering procedures using VCF file as input. Please open it with Notepad.