Bio::PopGen::HtSNP Bio::PopGen::HtSNP.pm module can select htSNP from a haplotype set.
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Perl module bioperl Bio Perl select htSNP PopGen HtSNP

Bio::PopGen::HtSNP Description

Bio::PopGen::HtSNP.pm module can select htSNP from a haplotype set. Bio::PopGen::HtSNP.pm module can select htSNP from a haplotype set.SYNOPSIS use Bio::PopGen::HtSNP; my $obj = Bio::PopGen::HtSNP->new($hap,$snp,$pop);Select the minimal set of SNP that contains the full information about the haplotype without redundancies.Take as input the followin values:- the haplotype block (array of array). - the snp id (array). - family information and frequency (array of array). The final haplotype is generated in a numerical format and the SNP's sets can be retrieve from the module.considerations:- If you force to include a family with indetermination, the SNP's with indetermination will be removed from the analysis, so consider before to place your data set what do you really want to do.- If two families have the same information (identical haplotype), one of them will be removed and the removed files will be stored classify as removed.- Only are accepted for calculation A, C, G, T and - (as deletion) and their combinations. Any other value as n or ? will be considered as degenerations due to lack of information. Requirements: · Perl

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