Scout annotation workflow

Snakemake workflow for annotating VCFs prior loading into Scout.

Setup

I recommend installing the package in a dedicated virtual environment.

python -m pip install .
scout-annotation --help
# Usage: scout-annotation [OPTIONS] COMMAND [ARGS]...
#
# Options:
#   -c, --config TEXT               config file used for overwriting defaults
#   -r, --resources TEXT            resources file for overwriting defaults
#   --cores INTEGER                 number of cores available for snakemake
#   --use-apptainer, --use-singularity
#                                   use apptainer as executor
#   --apptainer-args, --singularity-args TEXT
#                                   arguments for apptainer
#   --apptainer-prefix, --singularity-prefix TEXT
#                                   path to cached apptainer containers
#   --loglevel [DEBUG|INFO|WARNING|ERROR]
#                                   set logging level
#   --version                       Show the version and exit.
#   -h, --help                      Show this message and exit.
#
# Commands:
#   batch   Annotate a batch of samples.
#   panels  List available gene panels
#   single  Annotate a single sample.
#   trio    Annotate a trio of samples

Testing

This package is best managed by poetry, and tests are implemented using pytest.

poetry install
poetry run pytest

Running the above will run both unit tests and an integration test. Currently, the integration test is only expected to run properly on one of the RV servers where /storage is mounted. If /storage is not found, the integration tests will be skipped.

Rule graph

flowchart TB
    1[rename_samples] -->
        2[bcftools_reheader] -->
        3[decompose] -->
        4[normalize] -->
        5[vt_sort] -->
        6[vt_uniq] -->
        7[fix_vcf_af] --> 30{Part of trio?}

    30 -- yes -->
        31[merge_trio] -->  9

    31 --> 70[peddy]
    9 --> 70
    10 --> 70

    30 -- no --> 9

    9[bgzip] -->
        11[vep] -->
        12[vcfanno] -->
        14[most_severe_consequence]

    9 --> 10[tabix] --> 11[vep]

    2 -->
        29{PED file given?} -- no -->
        8[mock_ped]

    8 --> 11
    8 --> 21
    8 --> 23

    13[vcfanno_config] --> 12
    14[most_severe_consequence] -->
        15{Panels and/or filters?}
    15 -- only filter --> 17[vcf_filtering]
    15 -- panels --> 18[panel_filtering]
    18 --> 19{Filters too?}
    19 -- yes --> 17[vcf_filtering]
    19 -- no --> 20{Any variants left?}
    15 -- none --> 20

    17 --> 20

    20 -- no --> 21[copy_results]

    20 -- yes -->
        16[genmod_annotate] -->
        22[genmod_models] -->
        23[genmod_score] -->
        24[genmod_compound] -->
        26[bgzip] -->
        21 -->
        40[sample_config] -->
        41[family_config] -->
        28[all]

    26 --> 27[tabix] --> 21

    50{BAM files given?} -- yes -->
        51[link_bam] -->
        28

    51 --> 40
    70 --> 21

    30 -- yes -->
        80[madeline2_data] -->
        81[madeline2_svg] -->
        21
    29 -- yes --> 80

    60[genmod_rank_model] --> 23