- Genotype prediction with paralog detection - reads2snp reads2snp_wrapper.pl -alr $alr_file -out Reads2SNP_output -all Geno2pfas_output -mth $nb_thread -data Reads2SNP_species_data -mod $model -sharing $parameters_sharing -geno $output_genotype -mat $multi_alleles -min $min_coverage -fis $fis -gpv $min_post_probability -par $paraclean.paraclean_switch -dir $paraclean.dirichlet -thr $paraclean.threshold -spa $paraclean.skip_paralogous -err $paraclean.error -pre $paraclean.precision -opt $paraclean.optimizer -kun $paraclean.mask -pfc $pfasclean.pfasclean_switch -win $pfasclean.window_width -het $pfasclean.SNPdens_threshold -snp $pfasclean.H_threshold -exec galaxy -del yes > $Wrapper_log M1 M2 All Separate Shared Best Random Accepted Forbidden Tolerated Yes No Yes No Yes No PseudoNewtonOptimizer BFGS Yes No yes no **Reads2SNP Description** ----- This program is a Read2SNP wrapper. It split a multi .alr file into simple .alr files and successively run Reads2SNP C++ executable on those created sub files. All the individual result files are concatenated in a multi .alr_gen file which contains all the predicted genotypes (by position and individual) and the posterior probability of the each prediction. ----- **ParaClean Description** ----- ParaClean comes from the genofiltre.pl script written by Benoit Nabholz and Sylvain Glemin. Paraclean analyze each position of an input sequence and try to define if a given heterozygous position is a real heterozygous postion or a paralogous one (which comes from the erroneous assembly of two paralogs into a single contig). Real heterozygous status of a position is assessed through a likelihood ratio test between the two alternative hypothesis (paralogs vs heterozygotes). Models (multinomial or Dirichlet multinomial) parameters are the counts for each bases at a position in every individuals. The more the counts of two bases at a given position is far from 50/50 on different individuals (assuming there is no allelic expression bias), the more likely is the paralogous model. ---- **Pfasclean Description This program can be used to clean (ie. mask heterozygosity and SNP density bias) the multiple alignment. ----