Convert into genofile

  • See MagicBase.rabbitgeno_mma2jl for converting a Mathematica-version RABBIT genofile in CSV format into a julia-version RABBIT vcf genofile.

  • See MagicBase.arrayfile2vcf for converting a SNP array genofile into a vcf genofile. An array genofile is a CSV file with delim=',', consisting of one marker column plus one column for each sample. Each genotype cell is one of the combinations of alleles A, T, G, C, and - (missing allele).

  • See MagicBase.hapmap2vcf for converting a hapmap genofile into a vcf genofile. A hapmap genofile is a text file with extension ".hmp.txt" and delim='\t', consisting of 11 columns (rs#, alleles, chrom, pos, strand, assembly#, center, protLSID, assayLSID, panelLSID, QCcode) plus one column for each sample.

  • See MagicBase.merge_vcffiles for merging a list of vcf genofiles into a single vcf genofile.

  • See MagicBase.merge_arrayfiles for merging a list of SNP array genofiles into a single arrayfile.

Convert into pedfile

  • See MagicBase.rabbitped_mma2jl for converting a Mathematica-version RABBIT pedfile into a julia-version RABBIT pedfile.

  • See MagicBase.array_extract_pedfile for extracting a pedfile from an array file and a designcode for a non-subdivided population.

  • See MagicBase.vcf_extract_pedfile for extracting a pedfile from a vcf file and a designcode for a non-subdivided population.

  • See MagicBase.parsebreedped for converting a breedped file into a magicped file. A breedped file consists of three columns: individual, pedcode, and nself; the latter two columns constitute a designcode in form of breedcross (pedcode=>nself). Offspring with the same designcode forms a subpopulation.

  • See MagicBase.merge_pedfiles for merging a list of RABBIT (julia-version) pedfiles into a single pedfile.