Changes

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: Secondary and Supplementary reads are skipped when converting to FastQ.  It assumes that there will only be 2 reads (the 2 primary mates) with the same read name that are not secondary or supplementary.'''

'''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.'''

'''NOTE: Use the --splitRG option to split reads into read group specific FASTQs.'''

== How to use it ==

== How to use it ==