NAME
bam2fastx - tophat component converting bam directly into fastx
DESCRIPTION
bam2fastx v2.1.1 () usage:
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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,
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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
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convert all reads (mapped and unmapped) (but discarding those flagged as QC failed, unless -Q)
- -P
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paired reads are expected and converted into two output files (see <outfname> comments below)
- -Q
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convert unmapped reads even when flagged as QC failed
- -M,--maped-only
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convert only mapped reads
- -N
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for -P, append /1 and /2 suffixes to read names
- -O
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ignore the original quality values (OQ tag) and write the current quality values (default is to use OQ data if found)
- -C,--color
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reads are in ABI SOLiD color format
- -s,-t,--sam
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input is a SAM text file (default: BAM input expected)
- -a,--fasta
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output FASTA records, not FASTQ (discard quality values)
- -o <outfname>
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output file name or template (see below)
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<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.
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Example of converting all paired reads from a BAM file to FASTQ format:
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bam2fastx -PANQ -o sample.fq.gz sample.sortedbyname.bam
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In this example the output will be written in two files:
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sample.1.fq.gz and sample.2.fq.gz