Command Line Usage

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.