bam2fastx1

Overview

Options

-A,--all

convert all reads (mapped and unmapped) (but discarding those flagged as QC failed, unless -Q)

-P

paired reads are expected and converted into two output files (see <outfname> comments below)

-Q

convert unmapped reads even when flagged as QC failed

-M,--maped-only

convert only mapped reads

-N

for -P, append /1 and /2 suffixes to read names

-O

ignore the original quality values (OQ tag) and write the current quality values (default is to use OQ data if found)

-C,--color

reads are in ABI SOLiD color format

-s,-t,--sam

input is a SAM text file (default: BAM input expected)

-a,--fasta

output FASTA records, not FASTQ (discard quality values)

-o <outfname>

output file name or template (see below)

<outfname> serves as a name template when -P option is provided, as suffixes .1 and .2 will be automatically inserted before the file extension in <outfname>, such that two file names will be created. If <outfname> ends in .gz or .bz2 then bam2fastx will write the output compressed by gzip or bzip2 respectively.

Example of converting all paired reads from a BAM file to FASTQ format:

bam2fastx -PANQ -o sample.fq.gz sample.sortedbyname.bam

In this example the output will be written in two files:

sample.1.fq.gz and sample.2.fq.gz