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| = Parameters = | | = Parameters = |
| <pre> | | <pre> |
− | Required Parameters:
| + | Required Parameters: |
− | --in : the SAM/BAM file to convert to FastQ
| + | --in : the SAM/BAM file to convert to FastQ |
− | Optional Parameters:
| + | Optional Parameters: |
− | --readname : Process the BAM as readName sorted instead
| + | --readname : Process the BAM as readName sorted instead |
− | of coordinate if the header does not indicate a sort order.
| + | of coordinate if the header does not indicate a sort order. |
− | --merge : Generate 1 interleaved (merged) FASTQ for paired-ends (unpaired in a separate file)
| + | --splitRG : Split into RG specific fastqs. |
− | use firstOut to override the filename of the interleaved file.
| + | --qualField : Use the base quality from the specified tag |
− | --refFile : Reference file for converting '=' in the sequence to the actual base
| + | rather than from the Quality field (default) |
− | if '=' are found and the refFile is not specified, 'N' is written to the FASTQ
| + | --merge : Generate 1 interleaved (merged) FASTQ for paired-ends (unpaired in a separate file) |
− | --firstRNExt : read name extension to use for first read in a pair
| + | use firstOut to override the filename of the interleaved file. |
− | default is "/1"
| + | --refFile : Reference file for converting '=' in the sequence to the actual base |
− | --secondRNExt : read name extension to use for second read in a pair
| + | if '=' are found and the refFile is not specified, 'N' is written to the FASTQ |
− | default is "/2"
| + | --firstRNExt : read name extension to use for first read in a pair |
− | --rnPlus : Add the Read Name/extension to the '+' line of the fastq records
| + | default is "/1" |
− | --noReverseComp : Do not reverse complement reads marked as reverse
| + | --secondRNExt : read name extension to use for second read in a pair |
− | --noeof : Do not expect an EOF block on a bam file.
| + | default is "/2" |
− | --params : Print the parameter settings to stderr
| + | --rnPlus : Add the Read Name/extension to the '+' line of the fastq records |
− | Optional OutputFile Names:
| + | --noReverseComp : Do not reverse complement reads marked as reverse |
− | --outBase : Base output name for generated output files
| + | --region : Only convert reads containing the specified region/nucleotide. |
− | --firstOut : Output name for the first in pair file
| + | Position formatted as: chr:pos:base |
− | over-rides setting of outBase
| + | pos (0-based) & base are optional. |
− | --secondOut : Output name for the second in pair file
| + | --gzip : Compress the output FASTQ files using gzip |
− | over-rides setting of outBase
| + | --noeof : Do not expect an EOF block on a bam file. |
− | --unpairedOut : Output name for unpaired reads
| + | --params : Print the parameter settings to stderr |
− | over-rides setting of outBase
| + | Optional OutputFile Names: |
| + | --outBase : Base output name for generated output files |
| + | --firstOut : Output name for the first in pair file |
| + | over-rides setting of outBase |
| + | --secondOut : Output name for the second in pair file |
| + | over-rides setting of outBase |
| + | --unpairedOut : Output name for unpaired reads |
| + | over-rides setting of outBase |
| </pre> | | </pre> |
| | | |
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| | | |
| The file does not need to be strictly sorted by read name. The only requirement is that matching read names are next to each other. | | The file does not need to be strictly sorted by read name. The only requirement is that matching read names are next to each other. |
| + | |
| + | === Split into RG Specific FASTQs (<code>--splitRG</code>) === |
| + | |
| + | Create RG specific FASTQ files. |
| + | |
| + | Cannot be specified with firstOut/secondOut/unpairedOut since there will be a different filename for each RG. |
| + | |
| + | Cannot write to stdout when <code>--splitRG</code> is specified. |
| + | |
| + | Output filenames will be <outBase>.<RG>_1.fastq, <outBase>.<RG>_2.fastq, and <outBase>.<RG>.fastq. A fastq list file <outBase>.list will be created containing MERGE_NAME (the RG tag's SM value or outBase if the value is empty), fastq 1, fastq 2 (or . if it is a single ended fastq), and the RG tag string. |
| + | |
| + | === Use the Base Quality from the Specified Tag (<code>--qualField</code>) === |
| + | |
| + | By default, the quality field is used for the Base Qualities in the FASTQ file. Specify <code>--qualField <tagName></code> to use the base qualities from the specified tag instead of the quality field. |
| + | |
| | | |
| === Generate 1 Paired-End Output File (<code>--merge</code>) === | | === Generate 1 Paired-End Output File (<code>--merge</code>) === |
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| | | |
| Specifying <code>--noReverseComp</code> would result in a FASTQ sequence of ACCGTG | | Specifying <code>--noReverseComp</code> would result in a FASTQ sequence of ACCGTG |
| + | |
| + | === Only Convert the Specified Region (<code>--region</code>) === |
| + | |
| + | Only convert reads containing the specified region/nucleotide. |
| + | |
| + | Position formatted as: chr:pos:base |
| + | |
| + | pos (0-based) & base are optional. |
| | | |
| {{noeofBGZFParameter}} | | {{noeofBGZFParameter}} |