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The <code>bam2FastQ</code> option on the [[bamUtil]] converts a BAM file into FastQ files. This is necessary when only BAM files are delivered but a new alignment is desired. By converting BAM to FastQ files new alignments can be done using FastQ files
The <code>bam2FastQ</code> option on the [[bamUtil]] converts a BAM file into FastQ files. This is necessary when only BAM files are delivered but a new alignment is desired. By converting BAM to FastQ files new alignments can be done using FastQ files
NOTE: This tool does not work on templates that have more than 2 segments. It does not properly match reads when more than 2 reads have the same read name.
'''NOTE: This tool does not work on templates that have more than 2 segments. It does not properly match reads when more than 2 reads have the same read name.'''
'''NOTE: This tool does not split reads into read group specific FASTQs. If you want Read Group specific FASTQ files, first run [[BamUtil: splitBam]] to first split the BAM into 1 BAM per Read Group. Then run bam2FastQ on each bam.'''
== How to use it ==
== How to use it ==
Any errors and a summary of how many pairs and unpaired reads were processed are written to stderr.
Any errors and a summary of how many pairs and unpaired reads were processed are written to stderr.
NOTE: This tool does not work on templates that have more than 2 segments. It does not properly match reads when more than 2 reads have the same read name.
'''NOTE: This tool does not work on templates that have more than 2 segments. It does not properly match reads when more than 2 reads have the same read name.'''
'''NOTE: This tool does not split reads into read group specific FASTQs. If you want Read Group specific FASTQ files, first run [[BamUtil: splitBam]] to first split the BAM into 1 BAM per Read Group. Then run bam2FastQ on each bam.'''
=== Output Files ===
=== Output Files ===
