> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/postprocessing_variant_calls/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/postprocessing_variant_calls/cli.md). # Command Line Usage **Usage**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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 ...`: 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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**: ```console $ 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.