Overview

Transforms raw Illumina sequencing data into an unmapped SAM or BAM file. The IlluminaBaseCallsToSam program collects, demultiplexes, and sorts reads across all of the tiles of a lane via barcode to produce an unmapped SAM/BAM file. An unmapped BAM file is often referred to as a uBAM. All barcode, sample, and library data is provided in the LIBRARY_PARAMS file. Note, this LIBRARY_PARAMS file should be formatted according to the specifications indicated below. The following is an example of a properly formatted LIBRARY_PARAMS file: BARCODE_1 OUTPUT SAMPLE_ALIAS LIBRARY_NAME AAAAAAAA SA_AAAAAAAA.bam SA_AAAAAAAA LN_AAAAAAAA AAAAGAAG SA_AAAAGAAG.bam SA_AAAAGAAG LN_AAAAGAAG AACAATGG SA_AACAATGG.bam SA_AACAATGG LN_AACAATGG N SA_non_indexed.bam SA_non_indexed LN_NNNNNNNN The BARCODES_DIR file is produced by the ExtractIlluminaBarcodes tool for each lane of a flow cell.

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