This hosts multiple scripts necessary for filtering and processing 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.

Vardict

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.

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

Visual representation of how this module works:

Leveraging the PyVcf package the following filtering is performed:

Case 1: Single sample mode

Case 2: Case-control mode

Abbreviations

• TVF - Tumor Variant Fraction

• NVF - Normal Variant Fraction

• tmq - tumor minimum quality

• nmq - normal minimum quality

• tdp - total depth

• tad - total allele depth

Post-processing of variant calls

This package provides a variety of commands for manipulating different types of common outputs (e.g. mafs, vcf and txt files) from different bioinformatic variant callers such as mutect and vardict.

Supported File Types:

• maf

• vardict

Installation

For general use you can run: pip install postprocessing_variant_calls or a tagged version with pip install git+https://github.com/msk-access/postprocessing_variant_calls.git@<version>

For setting up a development environment please see the Setting up a Dev Environment section.

Usage

See CLI for commmand line usage of the package.

Setting up a Dev Environment

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

Contributing to Documentation

The Gitbook for this repository is configured so changes are written in Gitbook and synced with the docs branch.

To contribute to the documentation, you can write your changes in Gitbook, request a review, and merge the changes. Keep in mind, you will need access to the organization to contribute.

Each file-type supported should have a section in the Gitbook detailing the implementation of the file-type and a justification of it's operations. For example, the maf file-type has it's own section, which includes a description of how a maf is defined internally in the package and a justification of it's operations and how to use them.

Beyond file-type sections, you will also notice a section called cli, which lists all commands in the postprocessing_variant_calls package. Do not manually edit this section. This section is created using the typer-cli package, which uses the typer help parameters specified in typer commands to generate documentation. It is automatically updated by the git-action, .github/workflows/document_package.yml upon a push to the main branch. To make sure the cli.md document updates to include newly added commands, specify all relevant typer help parameters.

If you'd like to see a mock of your typer commands as they'll appear in the cli.md document, you can run: poetry run typer postprocessing_variant_calls.main utils docs > docs/cli.md in a properly configured dev environment. Note that this file should not be included in your PRs. The cli.md should be only updated through the git-action, .github/workflows/document_package.yml.

The sub-command pv maf allows users to perform post-processing on maf files. It has has six sub-commands: annotate, concat, filter, mergetsv, subset, tag.

INPUT AND OUTPUT DESCRIPTION

INPUT

At a minimum, each of these commands assumes a MAF file to be a well-defined object with the following characteristics:

• a delimited file where the delimiter is either a '\t' or a ','

• the file uses one of the following extension: '.maf', '.txt', '.csv', 'tsv'

• The delimited file at A minimum includes the following columns: "Chromosome","Start_Position","End_Position","Reference_Allele","Tumor_Seq_Allele2"

• The minimum listed columns can be combined into a unique ID for each row.

However, some commands and their sub-commands may require additional columns and may use specific rules in their processing of the MAF file.

OUTPUT

Output is a MAF file which is modified as per the operation of each command,

USAGE

For specifics on these criteria and rules, please find additional documentation on these commands below:

The sub-command pv maf allows users to perform post-processing on maf files. It has has six sub-commands: annotate, concat, filter, mergetsv, subset, tag.

At minimum each of these commands assumes a maf file to be a well-defined object with the following characteristics:

• a delimited file where the delimiter is either a '\t' or a ','

• the file uses one of the following extension: '.maf', '.txt', '.csv', 'tsv'

• The delimited file at minimum includes the following columns: "Chromosome","Start_Position","End_Position","Reference_Allele","Tumor_Seq_Allele2"

• The minimum listed columns can be combined into a unique id for each row.

These are the minimum requirements for a maf being used in these post-processing commands.

However, some commands and their sub-commands may require additional criteria of the maf file. Additionally, they may also use specific rules in their processsing of the maf file.

For specifics on these criteria and rules, please find additional documentation on these commands below:

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"

Usage:

$ main [OPTIONS] COMMAND [ARGS]...

Options:

• --version

• --install-completion: Install completion for the current shell.

• --show-completion: Show completion for the current shell, to copy it or customize the installation.

• --help: Show this message and exit.

Commands:

• maf: operations for manipulating maf files...

• mutect1: post-processing commands for MuTect...

• mutect2: post-processing commands for MuTect...

• vardict: post-processing commands for VarDict...

main maf

operations for manipulating maf files based on a given input.

Usage:

$ main maf [OPTIONS] COMMAND [ARGS]...

Options:

• --help: Show this message and exit.

Commands:

• annotate: annotate maf files based on a given input.

• concat: row-wise concatenation for maf files.

• filter: filter maf files based on a given input.

• mergetsv: merge a tsv file onto a maf by a shared id...

• subset: subset maf files.

• tag: tag maf files based on a given input.

main maf annotate

annotate maf files based on a given input.

Usage:

$ main maf annotate [OPTIONS] COMMAND [ARGS]...

Options:

• --help: Show this message and exit.

Commands:

• extract_blocklist: Extract values from an optional blocklist...

• mafbybed: annotate a maf column by a bed file.

• mafbytsv: annotate a maf column by a bed file.

main maf annotate extract_blocklist

Extract values from an optional blocklist file if provided. Used in SNVs/indels workflow.

Usage:

$ main maf annotate extract_blocklist [OPTIONS]

Options:

• -b, --blocklist_file FILE: Blocklist text file to extract values from. Needs to be in TSV format [required]

• -m, --maf FILE: MAF file to subset [required]

• -sep, --separator TEXT: Specify a separator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf annotate mafbybed

annotate a maf column by a bed file.

Usage:

$ main maf annotate mafbybed [OPTIONS]

Options:

• -m, --maf FILE: input maf file [required]

• -b, --bed FILE: bed file to annotate maf [required]

• -o, --output TEXT: output maf file [default: output.maf]

• -c, --cname TEXT: name for annotation column [default: annotation]

• --help: Show this message and exit.

main maf annotate mafbytsv

annotate a maf column by a bed file.

Usage:

$ main maf annotate mafbytsv [OPTIONS]

Options:

• -m, --maf FILE: MAF file to subset [required]

• -t, --tsv FILE: MAF file to subset [required]

• -o, --output PATH: Maf output file name. [default: output.maf]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• -oc, --outcome_column TEXT: name for outcome column [default: hotspot]

• -v, --values <TEXT TEXT>...: name for annotation column. Defaults to (Yes, No) [default: yes, no]

• --help: Show this message and exit.

main maf concat

row-wise concatenation for maf files.

Usage:

$ main maf concat [OPTIONS]

Options:

• -f, --files PATH: MAF file to concatenate. Default assumes MAFs are tsv. MAF inputs are specified here, or using paths parameter

• -p, --paths PATH: A text file containing paths of maf files to concatenate. Default assumes MAFs are tsv. MAF files are specified here, or using files parameter.

• -o, --output PATH: Maf output file name. [default: output.maf]

• -h, --header PATH: A header file containing the columns to concatenate input mafs on. It must be a subset of: Hugo_Symbol, Chromosome, Start_Position, End_Position, Reference_Allele, Tumor_Seq_Allele2. These are also the default columns used for concatenation

• -de, --deduplicate: deduplicate outputted maf file.

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf filter

filter maf files based on a given input.

Usage:

$ main maf filter [OPTIONS] COMMAND [ARGS]...

Options:

• --help: Show this message and exit.

Commands:

• access_filters: Filter a MAF file based on all the...

• access_remove_variants: Filter a MAF file based on all the...

• cmo_ch: Filter a MAF file based on all the parameters

• hotspot: filter a MAF file based on the presence of...

• mappable: Filter a MAF file to retain only mappable...

• non_common_variant: Filter a MAF file for common variants and...

• non_hotspot: filter a MAF file based on the presence of...

• not_complex: Filter a MAF filter for complex variants...

main maf filter access_filters

Filter a MAF file based on all the parameters listed in ACCESS filters python script

Usage:

$ main maf filter access_filters [OPTIONS]

Options:

• -f, --fillout_maf FILE: Fillout MAF file to subset (direct output from traceback subworkflow) [required]

• -a, --anno_maf FILE: Annotated MAF file to subset (direct input file from beginning of traceback subworkflow) [required]

• -o, --output PATH: Maf output file name. [default: output]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• -bl, --blocklist TEXT: Optional input blocklist file for access filtering criteria. [default: tsv]

• -ts, --tumor_samplename TEXT: Name of Tumor Sample [required]

• -ns, --normal_samplename TEXT: Name of MATCHED normal sample [required]

• --tumor_detect_alt_thres TEXT: The Minimum Alt depth required to be considered detected in fillout [default: 2]

• --tumor_detect_alt_thres TEXT: The Minimum Alt depth required to be considered detected in fillout [default: 2]

• --curated_detect_alt_thres TEXT: The Minimum Alt depth required to be considered detected in fillout [default: 2]

• --plasma_detect_alt_thres TEXT: The Minimum Alt depth required to be considered detected in fillout [default: 2]

• --tumor_TD_min TEXT: The Minimum Total Depth required in tumor to consider a variant Likely Germline [default: 20]

• --normal_TD_min TEXT: The Minimum Total Depth required in Matched Normal to consider a variant Germline [default: 20]

• --tumor_vaf_germline_thres TEXT: The threshold for variant allele fraction required in Tumor to be consider a variant Likely Germline [default: 0.4]

• --tumor_vaf_germline_thres TEXT: The threshold for variant allele fraction required in Matched Normal to be consider a variant Germline [default: 0.4]

• --tier_one_alt_min TEXT: The Minimum Alt Depth required in hotspots [default: 3]

• --tier_two_alt_min TEXT: The Minimum Alt Depth required in non-hotspots [default: 5]

• --min_n_curated_samples_alt_detected TEXT: The Minimum number of curated samples variant is detected to be flagged [default: 2]

• --tn_ratio_thres TEXT: Tumor-Normal variant fraction ratio threshold [default: 5]

• --help: Show this message and exit.

main maf filter access_remove_variants

Filter a MAF file based on all the parameters satisfied by the remove variants by annotations CWL script in the ACCESS pipeline

Usage:

$ main maf filter access_remove_variants [OPTIONS]

Options:

• -m, --maf FILE: MAF file to subset [required]

• -i, --intervals FILE: Intervals file containing rows of criterion to tag input MAF by [required]

• -o, --output PATH: Maf output file name. [default: output.maf]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf filter cmo_ch

Filter a MAF file based on all the parameters

Usage:

$ main maf filter cmo_ch [OPTIONS]

Options:

• -m, --maf FILE: MAF file to subset [required]

• -o, --output PATH: Maf output file name. [default: output.maf]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf filter hotspot

filter a MAF file based on the presence of Hotspot variants

Usage:

$ main maf filter hotspot [OPTIONS]

Options:

• -m, --maf FILE: MAF file to subset [required]

• -o, --output PATH: Maf output file name. [default: output.maf]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf filter mappable

Filter a MAF file to retain only mappable variants

Usage:

$ main maf filter mappable [OPTIONS]

Options:

• -m, --maf FILE: MAF file to subset [required]

• -o, --output PATH: Maf output file name. [default: output.maf]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf filter non_common_variant

Filter a MAF file for common variants and retain only uncommo variants

Usage:

$ main maf filter non_common_variant [OPTIONS]

Options:

• -m, --maf FILE: MAF file to subset [required]

• -o, --output PATH: Maf output file name. [default: output.maf]

• -sep, --separator TEXT: Specify a separator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf filter non_hotspot

filter a MAF file based on the presence of Hotspot variants

Usage:

$ main maf filter non_hotspot [OPTIONS]

Options:

• -m, --maf FILE: MAF file to subset [required]

• -o, --output PATH: Maf output file name. [default: output.maf]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf filter not_complex

Filter a MAF filter for complex variants and retain only simple variants

Usage:

$ main maf filter not_complex [OPTIONS]

Options:

• -m, --maf FILE: MAF file to subset [required]

• -o, --output PATH: Maf output file name. [default: output.maf]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf mergetsv

merge a tsv file onto a maf by a shared id column.

Usage:

$ main maf mergetsv [OPTIONS]

Options:

• -ma, --mafa FILE: MAF file to subset

• -mb, --mafb FILE: MAF

• -o, --output PATH: Maf output file name. [default: merged.maf]

• -id, --merge_id TEXT: id to merge mafs on. [default: id]

• -h, --how TEXT: Type of merge to be performed on mafs. Defaults to left. [default: left]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf subset

subset maf files.

Usage:

$ main maf subset [OPTIONS]

Options:

• -m, --maf FILE: MAF file to subset

• -i, --ids PATH: List of ids to search for in the 'Tumor_Sample_Barcode' column. Header of this file is 'sample_id'

• --sid TEXT: Identifiers to search for in the 'Tumor_Sample_Barcode' column. Can be given multiple times

• -o, --output TEXT: Name of the output file [default: output_subset.maf]

• -c, --cname TEXT: Name of the column header to be used for sub-setting [default: Tumor_Sample_Barcode]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf tag

tag maf files based on a given input.

Usage:

$ main maf tag [OPTIONS] COMMAND [ARGS]...

Options:

• --help: Show this message and exit.

Commands:

• access: Tag a variant in a MAF file based on...

• by_rules: Tag a variant in a MAF file based on...

• by_variant_classification: Tag filtered MAF file by variant...

• cmo_ch: Tag a variant in MAF file based on all the...

• common_variant: Tag a variant in a MAF file as common...

• germline_status: Tag a variant in a MAF file as germline...

• hotspots: Tag a variant in a MAF file based on...

• prevalence_in_cosmicDB: Tag a variant in a MAF file with...

• traceback: Generate combined count columns between...

• truncating_mut_in_TSG: Tag a truncating mutating variant in a MAF...

main maf tag access

Tag a variant in a MAF file based on criterion stated by the SNV/indels ACCESS pipeline workflow

Usage:

$ main maf tag access [OPTIONS]

Options:

• -m, --maf FILE: MAF file to tag [required]

• -r, --rules FILE: Intervals JSON file containing criterion to tag input MAF by [required]

• -h, --hotspots FILE: Text file containing hotspots to tag input MAF by [required]

• -o, --output PATH: Maf output file name. [default: output_tagged.maf]

• -sep, --separator TEXT: Specify a separator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf tag by_rules

Tag a variant in a MAF file based on criterion stated by an input rules.json JSON file

Usage:

$ main maf tag by_rules [OPTIONS]

Options:

• -m, --maf FILE: MAF file to tag [required]

• -r, --rules FILE: Intervals JSON file containing criterion to tag input MAF by [required]

• -o, --output PATH: Maf output file name. [default: output_tagged.maf]

• -sep, --separator TEXT: Specify a separator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf tag by_variant_classification

Tag filtered MAF file by variant classifications and subset into individual text files.

Usage:

$ main maf tag by_variant_classification [OPTIONS]

Options:

• -m, --maf FILE: filtered MAF file to split by annotations with [required]

• -tx_ref, --canonical_tx_ref FILE: Reference canonical transcript file [required]

• -o, --output_dir PATH: Output Directory to export individual text files to. [default: output_dir]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf tag cmo_ch

Tag a variant in MAF file based on all the parameters listed

Usage:

$ main maf tag cmo_ch [OPTIONS]

Options:

• -m, --maf FILE: MAF file to subset [required]

• -o, --output PATH: Maf output file name. [default: output.maf]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf tag common_variant

Tag a variant in a MAF file as common variant based on GNOMAD AF

Usage:

$ main maf tag common_variant [OPTIONS]

Options:

• -m, --maf FILE: MAF file to subset [required]

• -o, --output PATH: Maf output file name. [default: output.maf]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf tag germline_status

Tag a variant in a MAF file as germline based on VAF value

Usage:

$ main maf tag germline_status [OPTIONS]

Options:

• -m, --maf FILE: MAF file to subset [required]

• -o, --output PATH: Maf output file name. [default: output.maf]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf tag hotspots

Tag a variant in a MAF file based on hotspots file

Usage:

$ main maf tag hotspots [OPTIONS]

Options:

• -m, --maf FILE: MAF file to tag [required]

• -h, --hotspots FILE: Text file containing hotspots to tag input MAF by [required]

• -o, --output PATH: Maf output file name. [default: output_tagged.maf]

• -sep, --separator TEXT: Specify a separator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf tag prevalence_in_cosmicDB

Tag a variant in a MAF file with prevalence in COSMIC DB

Usage:

$ main maf tag prevalence_in_cosmicDB [OPTIONS]

Options:

• -m, --maf FILE: MAF file to subset [required]

• -o, --output PATH: Maf output file name. [default: output.maf]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• --help: Show this message and exit.

main maf tag traceback

Generate combined count columns between standard and simplex/duplex mafs

Usage:

$ main maf tag traceback [OPTIONS]

Options:

• -m, --maf FILE: MAF file to tag [required]

• -o, --output PATH: Maf output file name. [default: output.maf]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• -sheet, --samplesheet PATH: Samplesheets in nucleovar formatting. See README for more info: https://github.com/mskcc-omics-workflows/nucleovar/blob/main/README.md. Used to add fillout type information to maf. The sample_id and type columns must be present.

• --help: Show this message and exit.

main maf tag truncating_mut_in_TSG

Tag a truncating mutating variant in a MAF file based on its presence in the Tumor Suppressor Gene

Usage:

$ main maf tag truncating_mut_in_TSG [OPTIONS]

Options:

• -m, --maf FILE: MAF file to subset [required]

• -o, --output PATH: Maf output file name. [default: output.maf]

• -sep, --separator TEXT: Specify a seperator for delimited data. [default: tsv]

• --help: Show this message and exit.

main mutect1

post-processing commands for MuTect version 1.1.5 VCFs.

Usage:

$ main mutect1 [OPTIONS] COMMAND [ARGS]...

Options:

• --help: Show this message and exit.

Commands:

• case-control: Post-processing commands for case-control...

main mutect1 case-control

Post-processing commands for case-control filtering of MuTect version 1.1.5 VCF input file.

Usage:

$ main mutect1 case-control [OPTIONS] COMMAND [ARGS]...

Options:

• --help: Show this message and exit.

Commands:

• filter: This tool helps to filter MuTect version...

main mutect1 case-control filter

This tool helps to filter MuTect version 1.1.5 VCFs for case-control calling

Usage:

$ main mutect1 case-control filter [OPTIONS]

Options:

• -i, --inputVcf FILE: Input vcf generated by MuTect which needs to be processed [required]

• -i, --inputTxt FILE: Input Txt file generated by MuTect which needs to be processed [required]

• --refFasta FILE: Input reference fasta [required]

• --tsampleName TEXT: Name of the tumor sample. [required]

• -dp, --totalDepth INTEGER RANGE: Tumor total depth threshold [default: 20; x>=0]

• -ad, --alleledepth INTEGER RANGE: [default: 1; x>=0]

• -tnr, --tnRatio INTEGER RANGE: Tumor-Normal variant fraction ratio threshold [default: 1; x>=0]

• -vf, --variantFraction FLOAT RANGE: Tumor variant fraction threshold [default: 5e-05; x>=0]

• -o, --outDir TEXT: Full Path to the output dir

• --help: Show this message and exit.

main mutect2

post-processing commands for MuTect version 2 VCFs.

Usage:

$ main mutect2 [OPTIONS] COMMAND [ARGS]...

Options:

• --help: Show this message and exit.

Commands:

• case-control: Post-processing commands for filtering of...

main mutect2 case-control

Post-processing commands for filtering of MuTect version 2 VCF input file.

Usage:

$ main mutect2 case-control [OPTIONS] COMMAND [ARGS]...

Options:

• --help: Show this message and exit.

Commands:

• filter: This tool helps to filter MuTect version 2...

main mutect2 case-control filter

This tool helps to filter MuTect version 2 VCFs for case-control calling

Usage:

$ main mutect2 case-control filter [OPTIONS]

Options:

• -i, --inputVcf FILE: Input vcf generated by MuTect2 which needs to be processed [required]

• -it, --inputTxt FILE: Input Txt generated by MuTect which needs to be processed. NOTE, a Txt file will not be used for Mutect2 filtering as it is not provided in standard output. [default: /dev/null]

• --refFasta FILE: Input reference fasta [default: /dev/null]

• --tsampleName TEXT: Name of the tumor sample. [required]

• -dp, --totalDepth INTEGER RANGE: Tumor total depth threshold [default: 20; x>=0]

• -ad, --alleleDepth INTEGER RANGE: [default: 1; x>=0]

• -tnr, --tnRatio INTEGER RANGE: Tumor-Normal variant fraction ratio threshold [default: 1; x>=0]

• -vf, --variantFraction FLOAT RANGE: Tumor variant fraction threshold [default: 5e-05; x>=0]

• -o, --outDir TEXT: Full Path to the output dir

• --help: Show this message and exit.

main vardict

post-processing commands for VarDict version 1.4.6 VCFs.

Usage:

$ main vardict [OPTIONS] COMMAND [ARGS]...

Options:

• --help: Show this message and exit.

Commands:

• case-control: Post-processing commands for a...

• single: Post-processing commands for a single...

main vardict case-control

Post-processing commands for a case-controlled VarDict version 1.4.6 VCFs

Usage:

$ main vardict case-control [OPTIONS] COMMAND [ARGS]...

Options:

• --help: Show this message and exit.

Commands:

• filter: This tool helps to filter vardict version...

main vardict case-control filter

This tool helps to filter vardict version 1.4.6 VCFs for case control calling

Usage:

$ main vardict case-control filter [OPTIONS]

Options:

• -i, --inputVcf FILE: Input vcf generated by vardict which needs to be processed [required]

• --tsampleName TEXT: Name of the tumor Sample [required]

• -dp, --totalDepth INTEGER RANGE: Tumor total depth threshold [default: 20; x>=20]

• -ad, --alleledepth INTEGER RANGE: [x>=1]

• -tnr, --tnRatio INTEGER: Tumor-Normal variant fraction ratio threshold [default: 1]

• -vf, --variantFraction FLOAT: Tumor variant fraction threshold [default: 5e-05]

• -mq, --minQual INTEGER: Minimum variant call quality [default: 0]

• -fg, --filterGermline: Whether to remove calls without 'somatic' status

• -o, --outDir TEXT: Full Path to the output dir

• --help: Show this message and exit.

main vardict single

Post-processing commands for a single sample VarDict version 1.4.6 VCFs

Usage:

$ main vardict single [OPTIONS] COMMAND [ARGS]...

Options:

• --help: Show this message and exit.

Commands:

• filter: This tool helps to filter vardict version...

main vardict single filter

This tool helps to filter vardict version 1.4.6 VCFs for single sample calling

Usage:

$ main vardict single filter [OPTIONS]

Options:

• -i, --inputVcf FILE: Input vcf generated by vardict which needs to be processed [required]

• --tsampleName TEXT: Name of the tumor Sample [required]

• -dp, --totalDepth INTEGER RANGE: Tumor total depth threshold [default: 20; x>=20]

• -ad, --alleledepth INTEGER RANGE: [x>=1]

• -tnr, --tnRatio INTEGER: Tumor-Normal variant fraction ratio threshold [default: 1]

• -vf, --variantFraction FLOAT: Tumor variant fraction threshold [default: 5e-05]

• -mq, --minQual INTEGER: Minimum variant call quality [default: 0]

• -fg, --filterGermline: Whether to remove calls without 'somatic' status

• -o, --outDir TEXT: Full Path to the output dir

• --help: Show this message and exit.