DESCRIPTION

bam2fastx v2.1.1 () usage:

bam2fastx [--fasta|-a] [-C|--color] [-P|--paired] [-N] [-A|--all|-M|--mapped-only] [-Q] [--sam|-s|-t] [-o <outfname>] <in.bam>

By default, bam2fastx only converts the unmapped reads from the input file,

discarding those unmapped reads flagged as QC failed. The input BAM/SAM file MUST be sorted by read name (-n option for samtools sort). If the input file name is "-", stdin will be used instead.

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