Tools for working with genomic and high throughput sequencing data.
Group: Basecalling
Extracts sample and library information from an sample sheet for a given lane.
The sample sheet should be an Illumina Experiment Manager sample sheet. The tool writes two files to the output directory: a barcode parameter file and a library parameter file.
The barcode parameter file is used by Picard’s ExtractIlluminaBarcodes and CollectIlluminaBasecallingMetrics to
determine how to match sample barcodes to each read. The parameter file will be written to the output directory
with name barcode_params.<lane>.txt.
The library parameter file is used by Picard’s IlluminaBasecallsToSam to demultiplex samples and name the output
BAM file path for each sample output BAM file. The parameter file will be written to the output directory with name
library_params.<lane>.txt. The path to each sample’s BAM file will be specified in the library parameter
file. Each BAM file will have path <output>/<sample-name>.<barcode-sequence>.<lane>.bam.
| Name | Flag | Type | Description | Required? | Max # of Values | Default Value(s) |
|---|---|---|---|---|---|---|
| input | i | FilePath | The input sample sheet. | Required | 1 | |
| output | o | DirPath | The output folder to where per-lane parameter files should be written. | Required | 1 | |
| bam-output | b | DirPath | Optional output folder to where per-lane BAM files should be written, otherwise the output directory will be used. | Optional | 1 | |
| lanes | l | Int | The lane(s) (1-based) for which to write per-lane parameter files. | Required | Unlimited |