| SNiPlay3: a package for exploration and large scale analyses of SNP polymorphisms (filtering, density, vcftools, diversity, linkagedisequilibrium, GWAS) (does not include external tools) |
hg clone https://toolshed.g2.bx.psu.edu/repos/dereeper/sniplay
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Calculate SNP densities along chromosome from a VCF input | 2.0.0 | 16.01 | |
| Midpoint rooting of newick tree | 2.0.0 | 16.01 | |
| Calculates various diversity indexes with EggLib | 2.0.0 | 16.01 | |
| Converts a hapmap file into MLMM input files | 2.0.0 | 16.01 | |
| Get Haplotypes From Phased VCF | 2.0.0 | 16.01 | |
| Convert PED file to Fasta File | 2.0.0 | 16.01 | |
| Convert ped to bed | 2.0.0 | 16.01 | |
| Get annotation fromi a VCF file annotated by snpeff | 2.0.0 | 16.01 | |
| Checks concordance between input files for GWAS analysis | 2.0.0 | 16.01 | |
| Convert VCF to Hapmap | 2.0.0 | 16.01 | |
| IBS matrix / multi-dimensional scaling | 2.0.0 | 16.01 | |