Merge pull request #314 from NCI-CGR/data_catalog

BCF entry point with intensity and contamination checks using BCF for data_catalog usage.
NCI-CGR · Sep 25, 2024 · f2ff2c3 · f2ff2c3
2 parents fe64e33 + 58ed006
commit f2ff2c3
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diff --git a/docs/index.rst b/docs/index.rst
@@ -29,6 +29,7 @@ This lets us take advantage of snakemake_'s amazing workflow management system,
    :maxdepth: 1
 
    sub_workflows/entry_points
+   sub_workflows/intensity_check
    sub_workflows/contamination
    sub_workflows/sample_qc
    sub_workflows/subject_qc

diff --git a/docs/static/bcf_contamination.svg b/docs/static/bcf_contamination.svg
diff --git a/docs/static/bcf_intensity.svg b/docs/static/bcf_intensity.svg
diff --git a/docs/static/gtc_contamination.svg b/docs/static/gtc_contamination.svg
diff --git a/docs/static/idat_intensity.svg b/docs/static/idat_intensity.svg
diff --git a/docs/sub_workflows/contamination.rst b/docs/sub_workflows/contamination.rst
@@ -6,27 +6,28 @@ Contamination Sub-workflow
 **Workflow File**:
    https://github.com/NCI-CGR/GwasQcPipeline/blob/default/src/cgr_gwas_qc/workflow/sub_workflows/contamination.smk
 
+**Major Outputs**:
+
+   - ``sample_level/<BPM Prefix>.<software_params.contam_population>.abf.txt`` B allele frequencies from the 1000 genomes.
+   - ``sample_level/contamination/verifyIDintensity.csv`` aggregated table of contamination scores.
+
 **Config Options**: see :ref:`config-yaml` for more details
 
    - ``reference_files.thousand_genome_vcf``
    - ``reference_files.thousand_genome_tbi``
-   - ``user_files.gtc_pattern``
-   - ``user_files.idat_pattern``
+   - ``user_files.bcf`` or ( ``reference_files.illumina_manifest_file`` and ``user_files.gtc_pattern`` )
    - ``software_params.contam_population``
 
-**Major Outputs**:
-
-   - ``sample_level/<BPM Prefix>.<software_params.contam_population>.abf.txt`` B allele frequencies from the 1000 genomes.
-   - ``sample_level/contamination/median_idat_intensity.csv`` aggregated table of median IDAT intensities.
-   - ``sample_level/contamination/verifyIDintensity.csv`` aggregated table of contamination scores.
+|bcf_input_contamination| |gtc_input_contamination|
 
+.. |gtc_input_contamination| image:: ../static/gtc_contamination.svg
+   :width: 45%
 
-.. figure:: ../static/contamination.png
-   :name: fig-contamination-workflow
+.. |bcf_input_contamination| image:: ../static/bcf_contamination.svg
+   :width: 45%
 
-   The contamination sub-workflow.
-   This workflow will estimate contamination using verifyIDintensity on each sample individually.
-   It requires that you have GTC/IDAT files.
-   It first pulls B-allele frequencies from the 1000 Genomes VCF file.
-   It then estimate contamination for each sample and aggregates these results.
-   Finally, it also estimates the per sample median IDAT intensity, which is used to filter contamination results in the :ref:`sample-qc`
+The contamination sub-workflow.
+This workflow will estimate contamination using verifyIDintensity on each sample individually.
+It requires that you have aggregated BCF or GTC files.
+It first pulls B-allele frequencies from the 1000 Genomes VCF file.
+It then estimates contamination for each sample and aggregates these results.
diff --git a/docs/sub_workflows/entry_points.rst b/docs/sub_workflows/entry_points.rst
@@ -15,14 +15,15 @@ Entry Points Sub-workflow
    - ``user_files.bed``
    - ``user_files.bim``
    - ``user_files.fam``
+   - ``user_files.bcf``
 
 **Major Outputs**:
 
    - ``sample_level/samples.bed``
    - ``sample_level/samples.bim``
    - ``sample_level/samples.fam``
 
-There are three paths we can take to create these files:
+There are four paths we can take to create these files:
 
 1. If GTC files are provided using ``user_files.gtc_pattern`` then we will
 
@@ -34,3 +35,4 @@ There are three paths we can take to create these files:
 
 2. If an aggregated PED/MAP is provided using ``user_files.ped`` and ``user_files.map`` then we will convert the PED/MAP to BED/BIM/FAM.
 3. If an aggregated BED/BIM/FAM is provided using ``user_files.bed``, ``user_files.bim``, ``user_files.fam`` then we will create a symbolic link.
+4. If an aggregated BCF file is provided using ``user_files.bcf`` then we will convert the BCF to BED/BIM/FAM.