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todo
Lindsay Clark edited this page Jul 21, 2020
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This additional functionality should become available in future releases of polyRAD.
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Add functions to test if some loci need to be split into multiple loci due to duplication (e.g. disomic inheritance), and assign haplotypes from the old locus to the new loci.Included in v1.2 Export to VCF.-
Import from Stacks 2.0 when it is released.Included in v0.5 but needs testing. -
Add functions to filter out loci based on number of alleles per sample, and/or rule out possible ploidies based on number of alleles per sample.See Hind/He statistic in v1.2 -
Make pipelines and tutorials to go from raw sequencing data to polyRAD. This will not involve substantial changes to polyRAD itself, but rather building tools in TagDigger to help bridge the gap between other pipelines and polyRAD.Variant calling pipeline described in v1.2. - Allow specification of priors for breeding populations other than biparental populations, such as polycross populations.
- Accommodate markers with segregation distortion in priors for biparental mapping populations. (And in the way that parental genotypes are adjusted based on progeny allele frequencies.)
- Export to SPAGeDi and Structure.
- Get probabilities for multiallelic genotypes, not just pseudo-biallelic genotypes. A big job, possibly done in a new grant.
- Allow ploidy to vary by individual.
- Allow priors based on pedigrees.