# MuTect 1.1.5 ## Version of tools in docker image (/container/Dockerfile) | Tool | Version | Location | | -------------------- | ------- | --------------------------------------------------------------------------------------- | | openjdk:7 base image | 7 | - | | muTect | 1.1.5 | | ## CWL * CWL specification 1.0 * Use example\_inputs.yaml to see the inputs to the cwl * Example Command using [toil](https://toil.readthedocs.io): ```bash > toil-cwl-runner mutect_1.1.5.cwl example_inputs.yaml ``` **If at MSK, using the JUNO cluster you can use the following command** ```bash #Using CWLTOOL > cwltool --singularity --non-strict /path/to/mutect_1.1.5.cwl /path/to/inputs.yaml #Using toil-cwl-runner > mkdir mutect_toil_log > toil-cwl-runner --singularity --logFile /path/to/mutect_toil_log/cwltoil.log --jobStore /path/to/mutect_jobStore --batchSystem lsf --workDir /path/to/mutect_toil_log --outdir . --writeLogs /path/to/mutect_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/mutect_1.1.5.cwl /path/to/inputs.yaml > mutect_toil.stdout 2> mutect_toil.stderr & ``` ### Usage ``` usage: toil-cwl-runner mutect_1.1.5.cwl [-h] positional arguments: job_order Job input json file optional arguments: -h, --help show this help message and exit --BQSR BQSR The input covariates table file which enables on-the- fly base quality score recalibration --absolute_copy_number_data ABSOLUTE_COPY_NUMBER_DATA Absolute Copy Number Data, as defined by Absolute, to use in power calculations --arg_file ARG_FILE Reads arguments from the specified file --bam_tumor_sample_name BAM_TUMOR_SAMPLE_NAME if the tumor bam contains multiple samples, only use read groups with SM equal to this value --baq BAQ Type of BAQ calculation to apply in the engine (OFF|CALCULATE_AS_NECESSARY| RECALCULATE) --baqGapOpenPenalty BAQGAPOPENPENALTY BAQ gap open penalty (Phred Scaled). Default value is 40. 30 is perhaps better for whole genome call sets --clipping_bias_pvalue_threshold CLIPPING_BIAS_PVALUE_THRESHOLD pvalue threshold for fishers exact test of clipping bias in mutant reads vs ref reads --cosmic COSMIC VCF file of COSMIC sites --coverage_20_q20_file COVERAGE_20_Q20_FILE write out 20x of Q20 coverage in WIGGLE format to this file --coverage_file COVERAGE_FILE write out coverage in WIGGLE format to this file --dbsnp DBSNP VCF file of DBSNP information --dbsnp_normal_lod DBSNP_NORMAL_LOD LOD threshold for calling normal non-variant at dbsnp sites --defaultBaseQualities DEFAULTBASEQUALITIES If reads are missing some or all base quality scores, this value will be used for all base quality scores --disableRandomization Completely eliminates randomization from nondeterministic methods. To be used mostly in the testing framework where dynamic parallelism can result in differing numbers of calls to the generator. --disable_indel_quals If true, disables printing of base insertion and base deletion tags (with -BQSR) --downsample_to_coverage DOWNSAMPLE_TO_COVERAGE Target coverage threshold for downsampling to coverage --downsampling_type DOWNSAMPLING_TYPE Type of reads downsampling to employ at a given locus. Reads will be selected randomly to be removed from the pile based on the method described here (NONE|ALL_READS| BY_SAMPLE) given locus; note that downsampled reads are randomly selected from all possible reads at a locus --emit_original_quals If true, enables printing of the OQ tag with the original base qualities (with -BQSR) --enable_extended_output --excludeIntervals EXCLUDEINTERVALS One or more genomic intervals to exclude from processing. Can be explicitly specified on the command line or in a file (including a rod file) --filter_mismatching_base_and_quals if a read has mismatching number of bases and base qualities, filter out the read instead of blowing up. --force_alleles force output for all alleles at each site --force_output force output for each site --fraction_contamination FRACTION_CONTAMINATION estimate of fraction (0-1) of physical contamination with other unrelated samples --fraction_mapq0_threshold FRACTION_MAPQ0_THRESHOLD threshold for determining if there is relatedness between the alt and ref allele read piles --gap_events_threshold GAP_EVENTS_THRESHOLD how many gapped events (ins/del) are allowed in proximity to this candidate --gatk_key GATK_KEY GATK Key file. Required if running with -et NO_ET. Please see -phone-home-and-how-does-it-affect- me#latest for details. --heavily_clipped_read_fraction HEAVILY_CLIPPED_READ_FRACTION if this fraction or more of the bases in a read are soft/hard clipped, do not use this read for mutation calling --initial_tumor_lod INITIAL_TUMOR_LOD Initial LOD threshold for calling tumor variant --input_file_normal INPUT_FILE_NORMAL SAM or BAM file(s) --input_file_tumor INPUT_FILE_TUMOR SAM or BAM file(s) --interval_merging INTERVAL_MERGING Indicates the interval merging rule we should use for abutting intervals (ALL| OVERLAPPING_ONLY) --interval_padding INTERVAL_PADDING Indicates how many basepairs of padding to include around each of the intervals specified with the -L/ --interval_set_rule INTERVAL_SET_RULE Indicates the set merging approach the interval parser should use to combine the various -L or -XL inputs (UNION| INTERSECTION) --java_7 JAVA_7 --keep_program_records Should we override the Walkers default and keep program records from the SAM header --log_to_file LOG_TO_FILE Set the logging location --logging_level LOGGING_LEVEL Set the minimum level of logging, i.e. setting INFO gets you INFO up to FATAL, setting ERROR gets you ERROR and FATAL level logging. --maxRuntime MAXRUNTIME If provided, that GATK will stop execution cleanly as soon after maxRuntime has been exceeded, truncating the run but not exiting with a failure. By default the value is interpreted in minutes, but this can be changed by maxRuntimeUnits --maxRuntimeUnits MAXRUNTIMEUNITS The TimeUnit for maxRuntime (NANOSECONDS| MICROSECONDS|MILLISECONDS|SECONDS|MINUTES| HOURS|DAYS) --max_alt_allele_in_normal_fraction MAX_ALT_ALLELE_IN_NORMAL_FRACTION threshold for maximum alternate allele fraction in normal --max_alt_alleles_in_normal_count MAX_ALT_ALLELES_IN_NORMAL_COUNT threshold for maximum alternate allele counts in normal --max_alt_alleles_in_normal_qscore_sum MAX_ALT_ALLELES_IN_NORMAL_QSCORE_SUM threshold for maximum alternate allele quality score sum in normal --min_qscore MIN_QSCORE threshold for minimum base quality score --minimum_mutation_cell_fraction MINIMUM_MUTATION_CELL_FRACTION minimum fraction of cells which are presumed to have a mutation, used to handle non-clonality and contamination --minimum_normal_allele_fraction MINIMUM_NORMAL_ALLELE_FRACTION minimum allele fraction to be considered in normal, useful for normal sample contaminated with tumor --monitorThreadEfficiency Enable GATK threading efficiency monitoring --mutect MUTECT --nonDeterministicRandomSeed Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run --noop used for debugging, basically exit as soon as we get the reads --normal_depth_file NORMAL_DEPTH_FILE write out normal read depth in WIGGLE format to this file --normal_lod NORMAL_LOD LOD threshold for calling normal non-germline --normal_sample_name NORMAL_SAMPLE_NAME name to use for normal in output files --num_bam_file_handles NUM_BAM_FILE_HANDLES The total number of BAM file handles to keep open simultaneously --num_cpu_threads_per_data_thread NUM_CPU_THREADS_PER_DATA_THREAD How many CPU threads should be allocated per data thread to running this analysis? --num_threads NUM_THREADS How many data threads should be allocated to running this analysis. --only_passing_calls only emit passing calls --pedigree PEDIGREE Pedigree files for samples --pedigreeString PEDIGREESTRING Pedigree string for samples --pedigreeValidationType PEDIGREEVALIDATIONTYPE How strict should we be in validating the pedigree information? (STRICT|SILENT) --performanceLog PERFORMANCELOG If provided, a GATK runtime performance log will be written to this file --phone_home PHONE_HOME What kind of GATK run report should we generate? STANDARD is the default, can be NO_ET so nothing is posted to the run repository. Please see -phone-home- and-how-does-it-affect-me#latest for details. (NO_ET|STANDARD|STDOUT) --pir_mad_threshold PIR_MAD_THRESHOLD threshold for clustered read position artifact MAD --pir_median_threshold PIR_MEDIAN_THRESHOLD threshold for clustered read position artifact median --power_constant_af POWER_CONSTANT_AF Allelic fraction constant to use in power calculations --power_constant_qscore POWER_CONSTANT_QSCORE Phred scale quality score constant to use in power calculations --power_file POWER_FILE write out power in WIGGLE format to this file --preserve_qscores_less_than PRESERVE_QSCORES_LESS_THAN Bases with quality scores less than this threshold wont be recalibrated (with -BQSR) --read_buffer_size READ_BUFFER_SIZE Number of reads per SAM file to buffer in memory --read_filter READ_FILTER Specify filtration criteria to apply to each read individually --read_group_black_list READ_GROUP_BLACK_LIST Filters out read groups matching - or a .txt file containing the filter strings one per line. --reference_sequence REFERENCE_SEQUENCE --remove_program_records Should we override the Walkers default and remove program records from the SAM header --required_maximum_alt_allele_mapping_quality_score required minimum value for tumor alt allele maximum mapping quality score --somatic_classification_normal_power_threshold Power threshold for normal to determine germline vs variant --tag TAG Arbitrary tag string to identify this GATK run as part of a group of runs, for later analysis --tumor_depth_file TUMOR_DEPTH_FILE write out tumor read depth in WIGGLE format to this file --tumor_f_pretest TUMOR_F_PRETEST for computational efficiency, reject sites with allelic fraction below this threshold --tumor_lod TUMOR_LOD LOD threshold for calling tumor variant --tumor_sample_name TUMOR_SAMPLE_NAME name to use for tumor in output files --unsafe UNSAFE If set, enables unsafe operations - nothing will be checked at runtime. For expert users only who know what they are doing. We do not support usage of this argument. (ALLOW_UNINDEXED_BAM| ALLOW_UNSET_BAM_SORT_ORDER| NO_READ_ORDER_VERIFICATION| ALLOW_SEQ_DICT_INCOMPATIBILITY| LENIENT_VCF_PROCESSING|ALL) --useOriginalQualities If set, use the original base quality scores from the OQ tag when present instead of the standard scores --validation_strictness VALIDATION_STRICTNESS How strict should we be with validation (STRICT|LENIENT|SILENT) --vcf VCF VCF output of mutation candidates ``` --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://cmo-ci.gitbook.io/command-line-tools-cwl/develop-1/mutect/mutect_1.1.5.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.