codec
Category: CONSENSUS
Call CODEC consensus reads from grouped BAM
Arguments
| Flag | Description | Default |
|---|---|---|
-i, --input <INPUT> | Input BAM file | required |
-o, --output <OUTPUT> | Output BAM file | required |
--async-reader <ASYNC_READER> | Enable async userspace prefetch on the input BAM | false |
-r, --rejects <REJECTS> | Optional output BAM file for rejected reads | |
-s, --stats <STATS> | Optional output file for statistics | |
-p, --read-name-prefix <READ_NAME_PREFIX> | Prefix for consensus read names | |
-R, --read-group-id <READ_GROUP_ID> | Read group ID for consensus reads | A |
-1, --error-rate-pre-umi <ERROR_RATE_PRE_UMI> | Phred-scaled error rate prior to UMI integration | 45 |
-2, --error-rate-post-umi <ERROR_RATE_POST_UMI> | Phred-scaled error rate post UMI integration | 40 |
-m, --min-input-base-quality <MIN_INPUT_BASE_QUALITY> | Minimum base quality in raw reads to use for consensus | 10 |
-B, --output-per-base-tags <OUTPUT_PER_BASE_TAGS> | Produce per-base tags (cd, ce) in addition to per-read tags | true |
--trim <TRIM> | Quality-trim reads before consensus calling (removes low-quality bases from ends) | false |
--min-consensus-base-quality <MIN_CONSENSUS_BASE_QUALITY> | Minimum consensus base quality (output consensus bases below this are masked to N) | 2 |
--threads <THREADS> | Number of threads for the multi-threaded pipeline | |
--compression-level <COMPRESSION_LEVEL> | Compression level for output BAM (0-12) | 1 |
-M, --min-reads <MIN_READS> | Minimum read pairs per strand to form consensus (same as –min-reads) | 1 |
--max-reads <MAX_READS> | Maximum read pairs per strand (downsample if exceeded) | |
-d, --min-duplex-length <MIN_DUPLEX_LENGTH> | Minimum duplex overlap length in bases | 1 |
--single-strand-qual <SINGLE_STRAND_QUAL> | Reduce single-strand region quality to this value (0-93). Note: This uses a different short flag than duplex’s -q for min-base-quality | |
-Q, --outer-bases-qual <OUTER_BASES_QUAL> | Reduce outer bases quality to this value (0-93) | |
-O, --outer-bases-length <OUTER_BASES_LENGTH> | Number of outer bases to reduce quality for | 5 |
-x, --max-duplex-disagreement-rate <MAX_DUPLEX_DISAGREEMENT_RATE> | Maximum duplex disagreement rate (0.0-1.0) | 1.0 |
-X, --max-duplex-disagreements <MAX_DUPLEX_DISAGREEMENTS> | Maximum number of duplex disagreements | |
--scheduler <SCHEDULER> | Scheduler strategy for thread work assignment | balanced-chase-drain |
--pipeline-stats <PIPELINE_STATS> | Print detailed pipeline statistics at completion | false |
--deadlock-timeout <DEADLOCK_TIMEOUT> | Timeout in seconds for deadlock detection (default: 10, 0 = disabled) | 10 |
--deadlock-recover <DEADLOCK_RECOVER> | Enable automatic deadlock recovery (default: false, detection only) | false |
--queue-memory <QUEUE_MEMORY> | Pipeline queue memory limit per thread (default) or total | 768 |
--queue-memory-per-thread <QUEUE_MEMORY_PER_THREAD> | Interpret –queue-memory as per-thread (true, default) or total (false) | true |
--queue-memory-limit-mb <QUEUE_MEMORY_LIMIT_MB> | DEPRECATED: Use –queue-memory instead. Memory limit for pipeline queues in megabytes |