BaseRecalibrator v4.1.2.0

Version of tools in docker image

Tool	Version	Location
GATK	4.1.2.0	https://github.com/broadinstitute/gatk/releases/tag/4.1.2.0

CWL

• CWL specification 1.0

• Use example_inputs.yml to see the inputs to the cwl

• Example Command using toil:

    > toil-cwl-runner gatk_baserecalibrator_4.1.2.0.cwl example_inputs.yml

If at MSK, using the JUNO cluster you can use the following command

#Using CWLTOOL
> cwltool --singularity --non-strict gatk_baserecalibrator_4.1.2.0.cwl inputs.yaml

#Using toil-cwl-runner
> mkdir run_directory
> toil-cwl-runner --singularity --logFile path/to/run_directory/cwltoil.log  --jobStore path/to/jobStore --batchSystem lsf --workDir /path/to/run_directory --outdir /path/to/run_directory --writeLogs /path/to/run_directory --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 gatk_baserecalibrator_4.1.2.0.cwl inputs.yaml > file.stdout 2> file.stderr &

Usage

```bash

toil-cwl-runner gatk_baserecalibrator_4.1.2.0.cwl --help

usage: gatk_baserecalibrator_4.1.2.0.cwl [-h] --input INPUT --known_sites_1 KNOWN_SITES_1 --reference REFERENCE [--output_file_name OUTPUT_FILE_NAME] [--add_output_sam_program_record] [--add_output_vcf_command_line] [--arguments_file ARGUMENTS_FILE] [--binary_tag_name BINARY_TAG_NAME] [--bqsr_baq_gap_open_penalty BQSR_BAQ_GAP_OPEN_PENALTY] [--cloud-index-prefetch-buffer CLOUD_INDEX_PREFETCH_BUFFER] [--cloud_prefetch_buffer CLOUD_PREFETCH_BUFFER] [--create_output_bam_index] [--create_output_bam_md5] [--create_output_variant_index] [--create_output_variant_md5] [--default_base_qualities DEFAULT_BASE_QUALITIES] [--deletions_default_quality DELETIONS_DEFAULT_QUALITY] [--disable_bam_index_caching] [--disable_read_filter DISABLE_READ_FILTER] [--disable_sequence_dictionary_validation] [--exclude_intervals EXCLUDE_INTERVALS] [--gatk_config_file GATK_CONFIG_FILE] [--gcs_max_retries GCS_MAX_RETRIES] [--gcs_project_for_requester_pays GCS_PROJECT_FOR_REQUESTER_PAYS] [--indels_context_size INDELS_CONTEXT_SIZE] [--insertions_default_quality INSERTIONS_DEFAULT_QUALITY] [--interval_exclusion_padding INTERVAL_EXCLUSION_PADDING] [--interval_merging_rule INTERVAL_MERGING_RULE] [--interval_padding INTERVAL_PADDING] [--interval_set_rule INTERVAL_SET_RULE] [--intervals INTERVALS] [--lenient] [--low_quality_tail LOW_QUALITY_TAIL] [--maximum_cycle_value MAXIMUM_CYCLE_VALUE] [--mismatches_context_size MISMATCHES_CONTEXT_SIZE] [--mismatches_default_quality MISMATCHES_DEFAULT_QUALITY] [--preserve_qscores_less_than PRESERVE_QSCORES_LESS_THAN] [--quantizing_levels QUANTIZING_LEVELS] [--QUIET] [--read_filter READ_FILTER] [--read_index READ_INDEX] [--seconds_between_progress_updates SECONDS_BETWEEN_PROGRESS_UPDATES] [--sequence_dictionary SEQUENCE_DICTIONARY] [--sites_only_vcf_output] [--use_original_qualities] [--number_of_threads NUMBER_OF_THREADS] [--memory_per_job MEMORY_PER_JOB] [--memory_overhead MEMORY_OVERHEAD] [--known_sites_2 KNOWN_SITES_2] [job_order]

positional arguments: job_order Job input json file

optional arguments: -h, --help show this help message and exit --input INPUT BAM/SAM file containing reads --known_sites_1 KNOWN_SITES_1 One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis --reference REFERENCE Reference sequence file --output_file_name OUTPUT_FILE_NAME Output file name. Not Required --add_output_sam_program_record --add_output_vcf_command_line --arguments_file ARGUMENTS_FILE --binary_tag_name BINARY_TAG_NAME --bqsr_baq_gap_open_penalty BQSR_BAQ_GAP_OPEN_PENALTY --cloud-index-prefetch-buffer CLOUD_INDEX_PREFETCH_BUFFER --cloud_prefetch_buffer CLOUD_PREFETCH_BUFFER --create_output_bam_index --create_output_bam_md5 --create_output_variant_index --create_output_variant_md5 --default_base_qualities DEFAULT_BASE_QUALITIES --deletions_default_quality DELETIONS_DEFAULT_QUALITY --disable_bam_index_caching --disable_read_filter DISABLE_READ_FILTER --disable_sequence_dictionary_validation --exclude_intervals EXCLUDE_INTERVALS --gatk_config_file GATK_CONFIG_FILE --gcs_max_retries GCS_MAX_RETRIES --gcs_project_for_requester_pays GCS_PROJECT_FOR_REQUESTER_PAYS --indels_context_size INDELS_CONTEXT_SIZE --insertions_default_quality INSERTIONS_DEFAULT_QUALITY --interval_exclusion_padding INTERVAL_EXCLUSION_PADDING --interval_merging_rule INTERVAL_MERGING_RULE --interval_padding INTERVAL_PADDING --interval_set_rule INTERVAL_SET_RULE --intervals INTERVALS --lenient --low_quality_tail LOW_QUALITY_TAIL --maximum_cycle_value MAXIMUM_CYCLE_VALUE --mismatches_context_size MISMATCHES_CONTEXT_SIZE --mismatches_default_quality MISMATCHES_DEFAULT_QUALITY --preserve_qscores_less_than PRESERVE_QSCORES_LESS_THAN --quantizing_levels QUANTIZING_LEVELS --QUIET --read_filter READ_FILTER --read_index READ_INDEX --seconds_between_progress_updates SECONDS_BETWEEN_PROGRESS_UPDATES --sequence_dictionary SEQUENCE_DICTIONARY --sites_only_vcf_output --use_original_qualities --number_of_threads NUMBER_OF_THREADS --memory_per_job MEMORY_PER_JOB --memory_overhead MEMORY_OVERHEAD --known_sites_2 KNOWN_SITES_2