![]() Specifies the base call quality to output for N bases. Automatically added to fastq-n-quality for all output N bases.įilters output alignments with any bits set in val present in the flags field. If the RGSM entry matches the given Sample ID parameter for fastq-list.csv input, the option processes the entry.Įnables processing of all samples together, regardless of the RGSM value. Specifies CSV file that contains a list of FASTQ files to process. Specifies second FASTQ file with paired-end reads toinput. Specifies FASTQ file to input to the DRAGEN pipeline. Outputs a *.tbi index file in addition to the output VCF/gVCF. The default value is false.Įnables compression of VCF output files. If running the variant caller, the default value is false.Īutomatically adds tags related to methylation and outputs a single BAM for methylation protocols.Īutomatically detects paired-end parameters by running a sample through the mapper/aligner.Įnables variant deduplication. If only running map/align, the default value is true. files.Įnables the flagging of duplicate output alignment records.Įnables saving the output from the map/align stage. Imports subsequent segments of the *_001. Sets the path to the variant annotation database VCF (or *.vcf.gz) file. Specifies the CRAM file input for the DRAGEN variant caller. Uses alternative shared-thread ODIRECT file output. The default value is dynamically determined. ![]() Specifies the number of CPU threads for BCL input decompression. Specifies the number of CPU threads for output fastq.gz compression. Specifies the number of conversion threads per tile. Specifies the number of tiles to process in parallel. If set to false, the option prevents DRAGEN FPGA acceleration during BCL conversion. Specifies if unmapped reads are output to files marked as Undetermined. ![]() Specifies if all lanes of a flow cell are output to the same FASTQ files consecutively. The default is /RunInfo.xml.įor BCL conversion, the option outputs to subdirectories based on sample sheet Sample_Project column. The default value is false by default.Ĭonverts only the first tile of each lane during BCL conversion. ![]() The default location is the BCL root directory.įor BCL input, the option cancels analysis if any files are missing. By default, all lanes are converted.įor BCL input, the option sets the path to SampleSheet.csv file. Performs Illumina BCL conversion to FASTQ format.įor BCL input, the option converts only specified lane number. Specifies aligned BAM file for input to the DRAGEN variant caller. If alt liftover is used in a hash table, the option enables special processing for alt contigs. If a reference is built with liftover, the option is enabled by default.īy default, DRAGEN names both mate ends of pairs the same. When set to true, DRAGEN appends /1 and /2 to the two ends. ![]() Some mandatory fields must be specified on the command line and are not present in configuration files. The following options are in the default section of the configuration file. The default section is at the top of the configuration file and does not have a section name (eg, ) associated with it. ![]()
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