describe phenotypes in a separate page of the docs

docs/formats/genotypes.rst

@@ -0,0 +1,7 @@
+.. _formats-genotypes:
+
+
+Genotypes
+=========
+
+Genotype files must be specified as VCF or BCF files.

docs/formats/haplotypes.rst

@@ -1,8 +1,8 @@
 .. _formats-haplotypes:
 
 
-.hap
-====
+Haplotypes
+==========
 
 This document describes our custom file format specification for haplotypes: the ``.hap`` file.
 

docs/formats/phenotypes.rst

@@ -0,0 +1,28 @@
+.. _formats-phenotypes:
+
+
+Phenotypes and Covariates
+=========================
+
+Phenotype file format
+---------------------
+Phenotypes are expected to follow the PLINK2 ``.pheno`` file format. This is a
+tab-separated format where the first column corresponds to the sample ID, and
+subsequent columns contain each of your phenotypes.
+
+The first line of the file corresponds with the header and must begin with ``#IID``.
+The names of each of your phenotypes belong in the subbsequent columns of the header.
+
+See `tests/data/simple.pheno <https://github.com/gymrek-lab/haptools/blob/main/tests/data/simple.pheno>`_ for an example of a phenotype file:
+
+.. include:: ../../tests/data/simple.pheno
+   :literal:
+
+Covariate file format
+---------------------
+Covariates follow the same format as phenotypes.
+
+See `tests/data/simple.covar <https://github.com/gymrek-lab/haptools/blob/main/tests/data/simple.covar>`_ for an example of a covariate file:
+
+.. include:: ../../tests/data/simple.covar
+   :literal:

docs/index.rst

@@ -9,8 +9,9 @@
    :hidden:
    :maxdepth: 1
 
-   formats/inputs.rst
+   formats/genotypes.rst
    formats/haplotypes.rst
+   formats/phenotypes.rst
 
 .. toctree::
    :caption: Commands