ApplyBQSR 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_ApplyBQSR_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_ApplyBQSR_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_ApplyBQSR_4.1.2.0.cwl inputs.yaml > file.stdout 2> file.stderr &

Usage

```bash

toil-cwl-runner gatk_ApplyBQSR_4.1.2.0.cwl --help

usage: gatk_ApplyBQSR_4.1.2.0.cwl [-h] --reference REFERENCE [--create_output_bam_index] --bqsr_recal_file BQSR_RECAL_FILE --input INPUT [--output_file_name OUTPUT_FILE_NAME] [--add_output_sam_program_record] [--add_output_vcf_command_line] [--arguments_file ARGUMENTS_FILE] [--cloud_index_prefetch_buffer CLOUD_INDEX_PREFETCH_BUFFER] [--cloud_prefetch_buffer CLOUD_PREFETCH_BUFFER] [--create_output_bam_md5] [--create_output_variant_index] [--create_output_variant_md5] [--disable_bam_index_caching] [--disable_read_filter DISABLE_READ_FILTER] [--disable_sequence_dictionary_validation] [--emit_original_quals] [--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] [--global_qscore_prior GLOBAL_QSCORE_PRIOR] [--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] [--preserve_qscores_less_than PRESERVE_QSCORES_LESS_THAN] [--quantize_quals QUANTIZE_QUALS] [--quiet] [--read_filter READ_FILTER] [--read_index READ_INDEX] [--read_validation_stringency READ_VALIDATION_STRINGENCY] [--seconds_between_progress_updates SECONDS_BETWEEN_PROGRESS_UPDATES] [--sequence_dictionary SEQUENCE_DICTIONARY] [--sites_only_vcf_output] [--use_jdk_deflater] [--use_jdk_inflater] [--use_original_qualities] [--memory_overhead MEMORY_OVERHEAD] [--memory_per_job MEMORY_PER_JOB] [--number_of_threads NUMBER_OF_THREADS] [job_order]

positional arguments: job_order Job input json file

optional arguments: -h, --help show this help message and exit --reference REFERENCE Reference sequence --create_output_bam_index --bqsr_recal_file BQSR_RECAL_FILE Input recalibration table for BQSR. Only run ApplyBQSR with the covariates table created from the input BAM --input INPUT A BAM file containing input read data --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 --cloud_index_prefetch_buffer CLOUD_INDEX_PREFETCH_BUFFER --cloud_prefetch_buffer CLOUD_PREFETCH_BUFFER --create_output_bam_md5 --create_output_variant_index --create_output_variant_md5 --disable_bam_index_caching --disable_read_filter DISABLE_READ_FILTER --disable_sequence_dictionary_validation --emit_original_quals --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 --global_qscore_prior GLOBAL_QSCORE_PRIOR --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 --preserve_qscores_less_than PRESERVE_QSCORES_LESS_THAN --quantize_quals QUANTIZE_QUALS --quiet --read_filter READ_FILTER --read_index READ_INDEX --read_validation_stringency READ_VALIDATION_STRINGENCY --seconds_between_progress_updates SECONDS_BETWEEN_PROGRESS_UPDATES --sequence_dictionary SEQUENCE_DICTIONARY --sites_only_vcf_output --use_jdk_deflater --use_jdk_inflater --use_original_qualities --memory_overhead MEMORY_OVERHEAD --memory_per_job MEMORY_PER_JOB --number_of_threads NUMBER_OF_THREADS