Post-processing of variant calls

This hosts multiple scripts necessary for filtering and processing of variant calls in the vcfs/txt file generated by callers.

Callers Supported

pv is the main command for the postprocessing_variant_calls package see pv --help to see supported variant callers commands.

VarDictJava

The sub-command pv vardict allows users to perform post-processing on VarDictJava output. The two supported inputs to pv vardict from VarDictJava are single and case-control vcfs.

To specify to pv vardict, which input type will be used one of the following sub-commands may be used:

• pv vardict single for single sample vcfs
• pv vardict case-control for case-controlled vcfs.

Next the user can specify, what post-processing should be done. Right now, postprocessing_variant_calls supports filtering:

• pv vardict single filter
• pv vardict case-control filter

Finally, we can specify the paths and options for our filtering and run our command. Here is an example using the test data provided in this repository:

pv vardict single filter --inputVcf data/Myeloid200-1.vcf --tsampleName Myeloid200-1 -ad 1 -o data/single

There are various options and input specifications for filtering so see pv vardict single filter --help or pv vardict single case-sontrol --help for help.

See example_calls.sh for more example calls.

Maf

maf concat examples:

• pv maf concat -f path/to/maf1.maf -f path/to/maf2.maf -o output_maf
• pv maf concat -f path/to/maf1.maf -f path/to/maf2.maf -o output_maf -h header.txt where header.txt is a header file with names by which the mafs will be row-wise concatenated. See resources/header.txt for an example.
• pv maf -p path/to/paths.txt -o output/path/file where path/to/paths.txt is a txt file with maf path locations. See resources/paths.txt for an example.

maf annotate examples:

• pv maf mafbybed -m path/to/maf.maf -b path/to/maf.bed -o output/path/file -c annotation
• pv maf annotate mafbytsv -m /path/to/maf.(tsv/csv/maf) -t path/to/tsv.tsv -sep tsv -oc hotspot -v "Yes" "No"

maf tag examples:

• pv maf tag cmoch -m path/to/maf.maf -o output/path/file -sep "tsv"
• pv maf tag common_variant -m path/to/maf.maf -o output/path/file -sep "tsv"
• pv maf tag germline_status -m path/to/maf.maf -o output/path/file -sep "tsv"
• pv maf tag prevalence_in_cosmicDB -m path/to/maf.maf -o output/path/file -sep "tsv"
• pv maf tag truncating_mut_in_TSG -m path/to/maf.maf -o output/path/file -sep "tsv"

maf filter examples:

• pv maf filter cmo_ch -m path/to/maf.maf -o output/path/file -sep "tsv"
• pv maf filter hotspot -m path/to/maf.maf -o output/path/file -sep "tsv"
• pv maf filter mappable -m path/to/maf.maf -o output/path/file -sep "tsv"
• pv maf filter non_common_variant -m path/to/maf.maf -o output/path/file -sep "tsv"
• pv maf filter non_hotspot -m path/to/maf.maf -o output/path/file -sep "tsv"
• pv maf filter not_complex -m path/to/maf.maf -o output/path/file -sep "tsv"

How the repo was made

Template used: https://github.com/yxtay/python-project-template

Usage

Install External Dependencies

Have an environment with python >= 3.8 installed.

Install poetry:

pip install poetry

Install Package Dependencies

Then install project dependencies with Poetry.

cd /path/to/postprocessing_variant_calls
poetry install .

Accessing Environment

To access the environment after initial setup up run:

poetry shell