update docs to include GLIMPSE Hail Batch example

Author: LindoNkambule

docs/_build/doctrees/environment.pickle

@@ -38,9 +38,11 @@ Arguments and options
    * - Argument
      - Description
    * - :code:`--input-file`
-     - Path to where the VCF for target genotypes paths is
+     - Path to where the VCF or TSV with target VCF/BAM files is
    * - :code:`--vcf-ref`
      - Reference panel file to use for imputation
+   * - :code:`--chromosomes`
+     - Chromosome(s) to run imputation for. Default is :code:`all`
    * - :code:`--local`
      - Type of service. Default is Service backend where jobs are executed on a multi-tenant compute cluster in Google Cloud
    * - :code:`--billing-project`

docs/_build/doctrees/imputation.doctree

@@ -9,13 +9,21 @@ This is a short tutorial on how to use the different modules of GWASpy.
 1. Datasets
 ###########
 
-We will be using simulated test data (on GRCh37) from RICOPILI. Below is how it can be downloaded and copied to a Google bucket
+We will be using simulated test data (on GRCh37) from RICOPILI for most of the examples. Below is how it can be downloaded and copied to a Google bucket
 
     .. code-block:: sh
 
         wget https://personal.broadinstitute.org/sawasthi/share_links/UzoZK7Yfd7nTzIxHamCh1rSOiIOSdj_gwas-qcerrors.py/sim_sim1a_eur_sa_merge.miss.{bed,bim,fam} .
         gsutil cp sim_sim1a_eur_sa_merge.miss.{bed,bim,fam} gs://my-gcs/bucket/test_data
 
+For low-coverage genotype imputation using GLIMPSE, we will be using the 1X downsampled NA12878 file from the GLIMPSE
+tutorial. Below is how it can be downloaded and copied to a Google bucket
+
+    .. code-block:: sh
+
+        wget wget https://github.com/odelaneau/GLIMPSE/raw/refs/heads/master/tutorial/NA12878_1x_bam/NA12878.{bam,bam.bai} .
+        gsutil cp NA12878.{bam,bam.bai} gs://my-gcs/bucket/test_data
+
 2. Start a dataproc cluster with GWASpy installed
 #################################################
 
@@ -164,7 +172,32 @@ Now you can easily run both phasing and imputation using the following command
 
         ./nextflow run main.nf -c nextflow.config -profile gbatch -params-file params.json
 
-5. Low-coverage WGS imputation using GLIMPSE
+6. Low-coverage WGS imputation using GLIMPSE
 ############################################
 
+**6.1 Hail Batch** (should be ~$0.5 and takes <10 minutes)
+
+Unlike phasing using IMPUTE5, GLIMPSE takes BAM files as input, and since we usually have one BAM file per sample, the
+input to the imputation module when using GLIMPSE is a TSV file without a header and has two columns: first column with
+sample ID and second column with the actual path to the BAM file. Only one sample/BAM per row is allowed in the TSV.
+Below is an example of a file saved as :code:`gs://my-gcs/bucket/test_data/na12878_test.tsv`
+
+.. list-table::
+   :widths: 15 50
+   :header-rows: 0
+
+   * - NA12878
+     - gs://my-gcs/bucket/test_data/NA12878.bam
+
+
+Once you have saved the TSV to a bucket, you can run GLIMPSE phasing and imputation using the following command
+
+    .. code-block:: sh
+
+        imputation --input-file gs://my-gcs/bucket/test_data/na12878_test.tsv --vcf-ref hgdp1kgp \
+        --output-filename sim_sim1a_eur_sa_merge.miss_qced.phased.imputed \
+        --out-dir gs://my-gcs/bucket/test_data/GWASpy/lowcov_imputation --n-samples 1 --n-ref-samples 4091 \
+        --billing-project my-billing-project --chromosomes 22 --software glimpse2
+
+**6.2. Nextflow**
 **COMING VERY SOON**

docs/_build/doctrees/tutorial.doctree

@@ -122,30 +122,33 @@ <h2>Arguments and options<a class="headerlink" href="#arguments-and-options" tit
 </thead>
 <tbody>
 <tr class="row-even"><td><p><code class="code docutils literal notranslate"><span class="pre">--input-file</span></code></p></td>
-<td><p>Path to where the VCF for target genotypes paths is</p></td>
+<td><p>Path to where the VCF or TSV with target VCF/BAM files is</p></td>
 </tr>
 <tr class="row-odd"><td><p><code class="code docutils literal notranslate"><span class="pre">--vcf-ref</span></code></p></td>
 <td><p>Reference panel file to use for imputation</p></td>
 </tr>
-<tr class="row-even"><td><p><code class="code docutils literal notranslate"><span class="pre">--local</span></code></p></td>
+<tr class="row-even"><td><p><code class="code docutils literal notranslate"><span class="pre">--chromosomes</span></code></p></td>
+<td><p>Chromosome(s) to run imputation for. Default is <code class="code docutils literal notranslate"><span class="pre">all</span></code></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="code docutils literal notranslate"><span class="pre">--local</span></code></p></td>
 <td><p>Type of service. Default is Service backend where jobs are executed on a multi-tenant compute cluster in Google Cloud</p></td>
 </tr>
-<tr class="row-odd"><td><p><code class="code docutils literal notranslate"><span class="pre">--billing-project</span></code></p></td>
+<tr class="row-even"><td><p><code class="code docutils literal notranslate"><span class="pre">--billing-project</span></code></p></td>
 <td><p>Billing project to be used for the jobs</p></td>
 </tr>
-<tr class="row-even"><td><p><code class="code docutils literal notranslate"><span class="pre">--n-samples</span></code></p></td>
+<tr class="row-odd"><td><p><code class="code docutils literal notranslate"><span class="pre">--n-samples</span></code></p></td>
 <td><p>Number of target samples to be imputed. We use this to estimate resources for some of the jobs</p></td>
 </tr>
-<tr class="row-odd"><td><p><code class="code docutils literal notranslate"><span class="pre">--n-ref-samples</span></code></p></td>
+<tr class="row-even"><td><p><code class="code docutils literal notranslate"><span class="pre">--n-ref-samples</span></code></p></td>
 <td><p>Number of reference samples. We use this to estimate resources for some of the jobs</p></td>
 </tr>
-<tr class="row-even"><td><p><code class="code docutils literal notranslate"><span class="pre">--software</span></code></p></td>
+<tr class="row-odd"><td><p><code class="code docutils literal notranslate"><span class="pre">--software</span></code></p></td>
 <td><p>Software to use for phasing. Options: [<code class="code docutils literal notranslate"><span class="pre">beagle5</span></code>, <code class="code docutils literal notranslate"><span class="pre">impute5</span></code>]. Default is <code class="code docutils literal notranslate"><span class="pre">impute5</span></code></p></td>
 </tr>
-<tr class="row-odd"><td><p><code class="code docutils literal notranslate"><span class="pre">--output-filename</span></code></p></td>
+<tr class="row-even"><td><p><code class="code docutils literal notranslate"><span class="pre">--output-filename</span></code></p></td>
 <td><p>Output filename without file extension</p></td>
 </tr>
-<tr class="row-even"><td><p><code class="code docutils literal notranslate"><span class="pre">--out-dir</span></code></p></td>
+<tr class="row-odd"><td><p><code class="code docutils literal notranslate"><span class="pre">--out-dir</span></code></p></td>
 <td><p>Path to where output files will be saved</p></td>
 </tr>
 </tbody>

docs/_build/html/_sources/imputation.rst.txt

@@ -124,7 +124,7 @@ <h1>Contents<a class="headerlink" href="#contents" title="Link to this heading">
 <li class="toctree-l2"><a class="reference internal" href="tutorial.html#pre-imputation-qc">3. Pre-imputation QC</a></li>
 <li class="toctree-l2"><a class="reference internal" href="tutorial.html#pca">4. PCA</a></li>
 <li class="toctree-l2"><a class="reference internal" href="tutorial.html#phasing-and-imputation">5. Phasing and Imputation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorial.html#low-coverage-wgs-imputation-using-glimpse">5. Low-coverage WGS imputation using GLIMPSE</a></li>
+<li class="toctree-l2"><a class="reference internal" href="tutorial.html#low-coverage-wgs-imputation-using-glimpse">6. Low-coverage WGS imputation using GLIMPSE</a></li>
 </ul>
 </li>
 </ul>