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
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
Project details
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