diff --git a/README.rst b/README.rst index 20109f5..f6d57f0 100644 --- a/README.rst +++ b/README.rst @@ -63,11 +63,20 @@ estimated from depths. The output is reported as a simple VCF file which includes allele depths and population allele frequencies (estimated from the mean of individual frequencies), but no genotype calls. -Example notebooks ------------------ +Example notebook +---------------- -- An `example notebook`_ demonstrating genotype calling with MCHap in a bi-parental population. -- A `second example notebook`_ demonstrating some experimental features of MCHap presented at the 2024 `Tools for Polyploids`_ workshop. +See the `example notebook`_ demonstrating genotype calling with MCHap in a bi-parental population. + +Experimental features +--------------------- + + \:warning: **WARNING: The following tools are highly experimental!!!** :warning: + +- ``mchap call-pedigree``: for pedigree informed genotype calling. +- ``mchap atomize``: for converting micro-haplotype calls to phased sets of SNVs. + +See the `experimental notebook`_ demonstrating the `call-pedigree` tool as presented at the 2024 `Tools for Polyploids`_ workshop. Funding ------- @@ -81,5 +90,5 @@ The development of MCHap was partially funded by the "Tools for Polyploids" Spec .. _`MCHap assemble documentation`: docs/assemble.rst .. _`MCHap call documentation`: docs/call.rst .. _`example notebook`: docs/example/bi-parental.ipynb -.. _`second example notebook`: docs/example/bi-parental-pedigree.ipynb +.. _`experimental notebook`: docs/example/bi-parental-pedigree.ipynb .. _`Tools for Polyploids`: https://www.polyploids.org/ diff --git a/docs/example/bi-parental-pedigree.ipynb b/docs/example/bi-parental-pedigree.ipynb index b7468ef..4e8badd 100644 --- a/docs/example/bi-parental-pedigree.ipynb +++ b/docs/example/bi-parental-pedigree.ipynb @@ -10,7 +10,9 @@ "*(Last updated for MCHap version 0.10.0)*\n", "\n", "This notebook demonstrates pedigree informed micro-haplotype calling in a small bi-parental cross.\n", - "It uses a ***development release of MCHap***.\n", + "\n", + "**WARNING: The `call-pedigree` tool is considered highly experimental**!!!\n", + "\n", "The following topics are introduced:\n", "\n", "- **Pooled de novo haplotype assembly with `mchap assemble`**\n",