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bam2fastx - tophat component converting bam directly into fastx

BAM2FASTX(1) User Commands BAM2FASTX(1)

NAME

bam2fastx - tophat component converting bam directly into fastx

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
July 2017 bam2fastx 2.1.1+dfsg-3