BamUtil: bam2FastQ

Purpose

This 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

How to use it

When bam2FastQ is invoked without any arguments the following information is displayed

The following parameters are in effect:
           Input BAM/SAM File :                 (-iname)

Output FastQ Files
  Output : --first [], --second [], --single []

Required parameter

-i InputBAM/SAM

Optional parameters for output (however either --single or both --first and --second have to be provided)

--first firstReadInAPair_FastQ
--second secondReadInAPair_FastQ
--single unpairedReads_FastQ

In order to extract paired end reads, the BAM file has to be sorted by name, e.g. using samtools. Suppose the BAM file is myinput.bam

samtools sort -n myinput.bam myinput.sortByName.bam

Using sorted bam file to extract paired end fastq files

 bam2FastQ -i myinput.sortByName.BAM --first myread1.fastQ --second myread2.fastQ

Or to extract both paired end and single end fastq files (if the bam file contains both single and paired end reads)

 bam2FastQ -i myinput.sortByName.BAM --first myread1.fastQ --second myread2.fastQ --single myreadSingle.fastQ

Or using bam (sorted or not) file to extract single end fastq files

 bam2FastQ -i myinput.sortByName.BAM --single myreadSingle.fastQ