Merge pull request #67 from sbslee/0.17.0-dev

0.17.0 dev

Author: sbslee

CHANGELOG.rst

@@ -1,6 +1,15 @@
 Changelog
 *********
 
+0.17.0 (2022-07-12)
+-------------------
+
+* :issue:`63`: Fix bug in :meth:`api.utils.estimate_phase_beagle` when there is only one variant in input VCF and Beagle throws an error.
+* Update :command:`compare-genotypes` command to print the entire discordant calls when ``--verbose`` is used.
+* Update :command:`compute-copy-number` command to ensure that the samples in CovFrame[ReadDepth] and SampleTable[Statistics] are in the same order.
+* :issue:`64`: Update :meth:`api.utils.import_variants` method to 'diploidize' the input VCF when the target gene is G6PD. This is because some variant callers output haploid genotypes for males for the X chromosome, interfering with downstream analyses.
+* Remove unnecessary optional argument ``assembly`` from :meth:`api.core.get_ref_allele`.
+
 0.16.0 (2022-06-08)
 -------------------
 
@@ -71,7 +80,6 @@ Changelog
 * Deprecate :meth:`sdk.utils.parse_input_bams` method.
 * Update :meth:`api.utils.predict_alleles` method to match ``0.31.0`` version of ``fuc`` package.
 * Fix bug in :command:`filter-samples` command when ``--exclude`` argument is used for archive files with SampleTable type.
-* Remove unnecessary optional argument ``assembly`` from :meth:`api.core.get_ref_allele`.
 * Improve CNV caller for CYP2A6, CYP2B6, CYP2D6, CYP2E1, CYP4F2, GSTM1, SLC22A2, SULT1A1, UGT1A4, UGT2B15, and UGT2B17.
 * Add a new CNV call for CYP2D6: ``PseudogeneDeletion``.
 * In CYP2E1 CNV nomenclature, ``PartialDuplication`` has been renamed to ``PartialDuplicationHet`` and a new CNV call ``PartialDuplicationHom`` has been added. Furthermore, calling algorithm for CYP2E1\*S1 allele has been updated. When partial duplication is present, from now on the algorithm requires only \*7 to call \*S1 instead of both \*7 and \*4.

README.rst

@@ -177,6 +177,15 @@ you can access a development branch with the ``git checkout`` command. When
 you do this, please make sure your environment already has all the
 dependencies installed.
 
+.. note::
+    `Beagle <https://faculty.washington.edu/browning/beagle/beagle.html>`__
+    is one of the default software tools used by PyPGx for haplotype phasing
+    SNVs and indels. The program is freely available and published under the
+    `GNU General Public License <https://faculty.washington.edu/browning/
+    beagle/gpl_license>`__. Users do not need to download Beagle separately
+    because a copy of the software (``beagle.28Jun21.220.jar``) is already
+    included in PyPGx.
+
 .. warning::
     You're not done yet! Keep scrolling down to obtain the resource bundle
     for PyPGx, which is essential for running the package.
@@ -238,13 +247,13 @@ visually inspect SV calls. Below are CYP2D6 examples:
    * - Normal
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/gene-model-CYP2D6-1.png
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/GRCh37-CYP2D6-8.png
-   * - DeletionHet
+   * - WholeDel1
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/gene-model-CYP2D6-2.png
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/GRCh37-CYP2D6-1.png
-   * - DeletionHom
+   * - WholeDel1Hom
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/gene-model-CYP2D6-3.png
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/GRCh37-CYP2D6-6.png
-   * - Duplication
+   * - WholeDup1
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/gene-model-CYP2D6-4.png
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/GRCh37-CYP2D6-2.png
    * - Tandem3
@@ -254,6 +263,11 @@ visually inspect SV calls. Below are CYP2D6 examples:
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/gene-model-CYP2D6-10.png
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/GRCh37-CYP2D6-7.png
 
+PyPGx was recently applied to the entire high-coverage WGS dataset from 1KGP
+(N=2,504). Click `here <https://github.com/sbslee/1kgp-pgx-paper/tree/main/
+sv-tables>`__ to see individual SV calls, and corresponding copy number
+profiles and allele fraction profiles.
+
 GRCh37 vs. GRCh38
 =================
 

docs/create.py

@@ -204,6 +204,15 @@
 you do this, please make sure your environment already has all the
 dependencies installed.
 
+.. note::
+    `Beagle <https://faculty.washington.edu/browning/beagle/beagle.html>`__
+    is one of the default software tools used by PyPGx for haplotype phasing
+    SNVs and indels. The program is freely available and published under the
+    `GNU General Public License <https://faculty.washington.edu/browning/
+    beagle/gpl_license>`__. Users do not need to download Beagle separately
+    because a copy of the software (``beagle.28Jun21.220.jar``) is already
+    included in PyPGx.
+
 .. warning::
     You're not done yet! Keep scrolling down to obtain the resource bundle
     for PyPGx, which is essential for running the package.
@@ -265,13 +274,13 @@
    * - Normal
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/gene-model-CYP2D6-1.png
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/GRCh37-CYP2D6-8.png
-   * - DeletionHet
+   * - WholeDel1
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/gene-model-CYP2D6-2.png
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/GRCh37-CYP2D6-1.png
-   * - DeletionHom
+   * - WholeDel1Hom
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/gene-model-CYP2D6-3.png
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/GRCh37-CYP2D6-6.png
-   * - Duplication
+   * - WholeDup1
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/gene-model-CYP2D6-4.png
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/GRCh37-CYP2D6-2.png
    * - Tandem3
@@ -281,6 +290,11 @@
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/gene-model-CYP2D6-10.png
      - .. image:: https://raw.githubusercontent.com/sbslee/pypgx-data/main/dpsv/GRCh37-CYP2D6-7.png
 
+PyPGx was recently applied to the entire high-coverage WGS dataset from 1KGP
+(N=2,504). Click `here <https://github.com/sbslee/1kgp-pgx-paper/tree/main/
+sv-tables>`__ to see individual SV calls, and corresponding copy number
+profiles and allele fraction profiles.
+
 GRCh37 vs. GRCh38
 =================
 

docs/faq.rst

@@ -77,3 +77,49 @@ consistent with the other variant-level analyses you may also just use the
 same VCF for PyPGx. The bottom line is, if you are going to create your own
 input VCF, then you need to know what you are doing. Otherwise, it's probably
 safer to use :command:`create-input-vcf`.
+
+``chr22_KI270879v1_alt`` in GRCh38
+==================================
+
+Users may encounter an error like below when working with GRCh38 data:
+
+.. code-block:: text
+
+    $ pypgx prepare-depth-of-coverage \
+    depth-of-coverage.zip \
+    in.bam \
+    --assembly GRCh38
+    Traceback (most recent call last):
+      File "/Users/sbslee/opt/anaconda3/envs/fuc/bin/pypgx", line 33, in <module>
+        sys.exit(load_entry_point('pypgx', 'console_scripts', 'pypgx')())
+      File "/Users/sbslee/Desktop/pypgx/pypgx/__main__.py", line 33, in main
+        commands[args.command].main(args)
+      File "/Users/sbslee/Desktop/pypgx/pypgx/cli/prepare_depth_of_coverage.py", line 90, in main
+        archive = utils.prepare_depth_of_coverage(
+      File "/Users/sbslee/Desktop/pypgx/pypgx/api/utils.py", line 1247, in prepare_depth_of_coverage
+        cf = pycov.CovFrame.from_bam(bams, regions=regions, zero=True)
+      File "/Users/sbslee/Desktop/fuc/fuc/api/pycov.py", line 345, in from_bam
+        results += pysam.depth(*(bams + args + ['-r', region]))
+      File "/Users/sbslee/opt/anaconda3/envs/fuc/lib/python3.9/site-packages/pysam/utils.py", line 69, in __call__
+        raise SamtoolsError(
+    pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=samtools depth: cannot parse region "chr22_KI270879v1_alt:267307-281486"\n'
+
+This is a GRCh38-specific issue. One of the genes with SV is GSTT1 and it is
+located in the contig ``chr22_KI270879v1_alt``, which is missing in input BAM
+file. That's why the :command:`prepare-depth-of-coverage` command is
+complaining. To solve this issue, you can either re-align sequence reads in
+the presence of the contig in your FASTA reference genome or work around it
+by excluding GSTT1 from your analysis:
+
+.. code-block:: text
+
+    $ pypgx prepare-depth-of-coverage \
+    depth-of-coverage.zip \
+    in.bam \
+    --assembly GRCh38 \
+    --genes GSTT1 \
+    --exclude
+
+For more details, please see the following articles:
+:ref:`readme:GRCh37 vs. GRCh38` and :ref:`genes:GRCh38 data for GSTT1`.
+Related GitHub issues: :issue:`65`.