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:
> toil-cwl-runner mutect_1.1.5.cwl example_inputs.yamlIf at MSK, using the JUNO cluster you can use the following command
#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 <TAG> -<STRING> 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
<required_maximum_alt_allele_mapping_quality_score>
tumor alt allele maximum mapping quality score
--somatic_classification_normal_power_threshold
Power threshold for normal to
<somatic_classification_normal_power_threshold>
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 candidatesLast updated