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BamUtil: bam2FastQ

100 bytes removed, 23:35, 5 March 2016
Overview of the bam2FastQ function of bamUtil
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 segmentsSecondary and Supplementary reads are skipped when converting to FastQ. It does not properly match assumes that there will only be 2 reads when more than (the 2 reads have primary mates) with the same read namethat are not secondary or supplementary.'''
'''NOTE: This tool does not Use the --splitRG option to 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 ==

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