Skip to content

Commit

Permalink
fix rtd?
Browse files Browse the repository at this point in the history
  • Loading branch information
brentp committed Jan 12, 2016
1 parent e4ad650 commit 7cc53a5
Showing 1 changed file with 5 additions and 3 deletions.
8 changes: 5 additions & 3 deletions docs/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -9,13 +9,15 @@ in `.ped` files and the relationships inferred from a
corresponding `.vcf` file such as can occur from sample-swaps
or pedigree misspecifications.

The code to do this is quite simple. But we can automate using the command-line.
Below, we check for pedigree
The python code to do this is quite simple. But we can automate multiple
checks using the command-line interface. Below, we check for pedigree
violations by looking at 5,000 sites (see :doc:`relatedness <relatedness>`
for more details on selection) and for sex discrepancies by looking at the
non-PA regions of the X chromosome where males should have very few HET calls.

.. code-block::
The command-line usage looks like:

.. code-block:: bash
python -m pedagree --plot --prefix ceph-1463 ceph1463.vcf.gz ceph1463.ped
Expand Down

0 comments on commit 7cc53a5

Please sign in to comment.