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usage: fgbio_call_duplex_consensus_reads_1.2.0.cwl [-h]
[--memory_per_job MEMORY_PER_JOB]
[--memory_overhead MEMORY_OVERHEAD]
[--number_of_threads NUMBER_OF_THREADS]
--input INPUT
[--output_file_name OUTPUT_FILE_NAME]
[--read_name_prefix READ_NAME_PREFIX]
[--read_group_id READ_GROUP_ID]
[--error_rate_pre_umi ERROR_RATE_PRE_UMI]
[--error_rate_post_umi ERROR_RATE_POST_UMI]
[--min_input_base_quality MIN_INPUT_BASE_QUALITY]
[--trim]
[--sort_order SORT_ORDER]
[--min_reads MIN_READS]
[--max_reads_per_strand MAX_READS_PER_STRAND]
[--threads THREADS]
[job_order]
positional arguments:
job_order Job input json file
optional arguments:
-h, --help show this help message and exit
--memory_per_job MEMORY_PER_JOB
Memory per job in megabytes
--memory_overhead MEMORY_OVERHEAD
Memory overhead per job in megabytes
--number_of_threads NUMBER_OF_THREADS
--input INPUT The input SAM or BAM file.
--output_file_name OUTPUT_FILE_NAME
Output SAM or BAM file to write consensus reads.
--read_name_prefix READ_NAME_PREFIX
The prefix all consensus read names
--read_group_id READ_GROUP_ID
The new read group ID for all the consensus reads.
--error_rate_pre_umi ERROR_RATE_PRE_UMI
The Phred-scaled error rate for an error prior to the
UMIs being integrated.
--error_rate_post_umi ERROR_RATE_POST_UMI
The Phred-scaled error rate for an error post the UMIs
have been integrated.
--min_input_base_quality MIN_INPUT_BASE_QUALITY
Ignore bases in raw reads that have Q below this
value.
--trim If true, quality trim input reads in addition to
masking low Q bases
--sort_order SORT_ORDER
The sort order of the output, if :none: then the same
as the input.
--min_reads MIN_READS
The minimum number of input reads to a consensus read.
--max_reads_per_strand MAX_READS_PER_STRAND
The maximum number of reads to use when building a
single-strand consensus. If more than this many reads
are present in a tag family, the family is randomly
downsampled to exactly max-reads reads.