This hosts multiple scripts necessary for filtering and processing of variant calls in the vcfs/txt file generated by callers.
Project description
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 vcfspv 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
whereheader.txt
is a header file with names by which the mafs will be row-wise concatenated. Seeresources/header.txt
for an example.pv maf -p path/to/paths.txt -o output/path/file
wherepath/to/paths.txt
is a txt file with maf path locations. Seeresources/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
How the repo was made
Template used: https://github.com/yxtay/python-project-template
Usage
External dependencies
- [Conda][conda]
- [Docker][docker]
- [Make][make]
Create environment
Use Conda to create a virtual environment and activate it for the project.
conda env create -f environment.yml
conda activate pv_calls
Install dependencies
Then install project dependencies with Poetry.
make deps-install
Updating Environment
To update the environment after initial setup up run:
conda env update -f environment.yml
instead of conda create
, and then re-run make deps-install
Project details
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