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= Overview of the <code>bam2FastQ</code> function of <code>[[bamUtil]]</code> =
= Overview of the <code>bam2FastQ</code> function of <code>[[bamUtil]]</code> =
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.
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.
=== Output Files ===
=== Output Files ===
