Applies a trimming pipeline to any kind of sources for ReadTools
Description
Applies a trimming/filtering pipeline to the reads:
- Trimmers are applied in order. If ay read is trimmed completely, other trimmers are ignored.
- Filter out completely trim reads.
- Apply the filters in order. If any read is filtered, the FT tag reflects the ReadFilter involved.
Warning: Default trimmers/filters are applied before any other user-specified
trimmers/filters. If you would like to apply them in a different order, use
--disableAllDefaultTrimmers/--disableAllDefaultFilters in combination
with the new ordering. Note: Default arguments perform the same algorithm as the one described in
Kofler et al. (2011). Other features in their implementation could be applied with
some minor modifications in the command line.
Arguments
Required Arguments
| Argument name(s) | Type | Description |
|---|---|---|
--input-I |
String | BAM/SAM/CRAM/FASTQ source of reads. |
--output-O |
String | Output SAM/BAM/CRAM file. |
Optional Arguments
| Argument name(s) | Type | Default value(s) | Description |
|---|---|---|---|
--arguments_file |
List[File] | [] | read one or more arguments files and add them to the command line |
--disable3pTrim-D3PT |
boolean | false | Disable 3’-trimming. Cannot be true when argument disable5pTrim (D5PT) is true. |
--disable5pTrim-D5PT |
boolean | false | Disable 5’-trimming. May be useful for downstream mark of duplicate reads, usually identified by the 5’ mapping position. Cannot be true when disable3pTrim (D3P) is true. |
--disableAllDefaultTrimmers-disableAllDefaultTrimmers |
boolean | false | Disable all default trimmers. It may be useful to reorder the trimmers. |
--disableReadFilter-DF |
List[String] | [] | Read filters to be disabled after trimming |
--disableToolDefaultReadFilters-disableToolDefaultReadFilters |
boolean | false | Disable all tool default read filters for trimming |
--disableTrimmer-DTM |
Set[String] | [] | Default trimmers to be disabled. |
--gcs_max_retries-gcs_retries |
int | 20 | If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection |
--help-h |
boolean | false | display the help message |
--keepDiscarded-keepDiscarded |
boolean | false | Keep discarded reads in a separate file. Note: For pair-end input, this file contain also mates of discarded reads (they do not have FT tag). |
--readFilter-RF |
List[String] | [] | Read filters to be applied after trimming |
--trimmer-TM |
List[String] | [] | Trimmers to be applied. Note: default trimmers are applied first and then the rest of them in order. |
--version |
boolean | false | display the version number for this tool |
Optional Common Arguments
| Argument name(s) | Type | Default value(s) | Description |
|---|---|---|---|
--addOutputSAMProgramRecord-addOutputSAMProgramRecord |
boolean | true | If true, adds a PG tag to created SAM/BAM/CRAM files. |
--createOutputBamIndex-OBI |
boolean | true | If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. |
--createOutputBamMD5-OBM |
boolean | false | If true, create a MD5 digest for any BAM/SAM/CRAM file created |
--forceEncoding-forceEncoding |
FastqQualityFormat | null | Force original quality encoding of the input files. Possible values: Solexa, Illumina, Standard |
--forceOverwrite-forceOverwrite |
Boolean | false | Force output overwriting if it exists |
--input2-I2 |
String | null | BAM/SAM/CRAM/FASTQ the second source of reads (if pair-end). |
--interleavedInput-interleaved |
boolean | false | Interleaved input. |
--QUIET |
Boolean | false | Whether to suppress job-summary info on System.err. |
--readValidationStringency-VS |
ValidationStringency | SILENT | Validation stringency for all SAM/BAM/CRAM files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. Possible values: STRICT, LENIENT, SILENT |
--reference-R |
String | null | Reference sequence file. Required for CRAM input. |
--secondsBetweenProgressUpdates-secondsBetweenProgressUpdates |
double | 10.0 | Output traversal statistics every time this many seconds elapse. |
--TMP_DIR |
List[File] | [] | Undocumented option |
--use_jdk_deflater-jdk_deflater |
boolean | false | Whether to use the JdkDeflater (as opposed to IntelDeflater) |
--use_jdk_inflater-jdk_inflater |
boolean | false | Whether to use the JdkInflater (as opposed to IntelInflater) |
--verbosity-verbosity |
LogLevel | INFO | Control verbosity of logging. Possible values: ERROR, WARNING, INFO, DEBUG |
Advanced Arguments
| Argument name(s) | Type | Default value(s) | Description |
|---|---|---|---|
--showHidden-showHidden |
boolean | false | display hidden arguments |