samtools-fasta - Man Page

samtools fastq [options] in.bam
samtools fasta [options] in.bam

Converts a BAM or CRAM into either FASTQ or FASTA format depending on the command invoked. The files will be automatically compressed if the file names have a .gz or .bgzf extension.

If the input contains read-pairs which are to be interleaved or written to separate files in the same order, then the input should be first collated by name. Use samtools collate or samtools sort -n to ensure this.

For each different QNAME, the input records are categorised according to the state of the READ1 and READ2 flag bits. The three categories used are:

1 : Only READ1 is set.

2 : Only READ2 is set.

0 : Either both READ1 and READ2 are set; or neither is set.

The exact meaning of these categories depends on the sequencing technology used. It is expected that ordinary single and paired-end sequencing reads will be in categories 1 and 2 (in the case of paired-end reads, one read of the pair will be in category 1, the other in category 2). Category 0 is essentially a “catch-all” for reads that do not fit into a simple paired-end sequencing model.

For each category only one sequence will be written for a given QNAME. If more than one record is available for a given QNAME and category, the first in input file order that has quality values will be used. If none of the candidate records has quality values, then the first in input file order will be used instead.

Sequences will be written to standard output unless one of the -1, -2, -o, or -0 options is used, in which case sequences for that category will be written to the specified file. The same filename may be specified with multiple options, in which case the sequences will be multiplexed in order of occurrence.

If a singleton file is specified using the -s option then only paired sequences will be output for categories 1 and 2; paired meaning that for a given QNAME there are sequences for both category 1 and 2. If there is a sequence for only one of categories 1 or 2 then it will be diverted into the specified singletons file. This can be used to prepare fastq files for programs that cannot handle a mixture of paired and singleton reads.

The -s option only affects category 1 and 2 records. The output for category 0 will be the same irrespective of the use of this option.

-n

By default, either '/1' or '/2' is added to the end of read names where the corresponding READ1 or READ2 FLAG bit is set. Using -n causes read names to be left as they are.

-N

Always add either '/1' or '/2' to the end of read names even when put into different files.

-O

Use quality values from OQ tags in preference to standard quality string if available.

-s FILE

Write singleton reads to FILE.

-t

Copy RG, BC and QT tags to the FASTQ header line, if they exist.

-T TAGLIST

Specify a comma-separated list of tags to copy to the FASTQ header line, if they exist.

-1 FILE

Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them. If the -s option is used, only paired reads will be written to this file.

-2 FILE

Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them. If the -s option is used, only paired reads will be written to this file.

-o FILE

Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout.  This is equivalent to -1 FILE -2 FILE.

-0 FILE

Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE instead of outputting them.

-f INT

Only output alignments with all bits set in INT present in the FLAG field. INT can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' (i.e. /^0[0-7]+/) [0].

-F INT

Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' (i.e. /^0[0-7]+/) [0x900]. This defaults to 0x900 representing filtering of secondary and supplementary alignments.

-G INT

Only EXCLUDE reads with all of the bits set in INT present in the FLAG field. INT can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' (i.e. /^0[0-7]+/) [0].

-i

add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)

-c [0..9]

set compression level when writing gz or bgzf fastq files.

--i1 FILE

write first index reads to FILE

--i2 FILE

write second index reads to FILE

--barcode-tag TAG

aux tag to find index reads in [default: BC]

--quality-tag TAG

aux tag to find index quality in [default: QT]

-@,  --threads INT

Number of input/output compression threads to use in addition to main thread [0].

--index-format STR

string to describe how to parse the barcode and quality tags. For example:

i14i8

the first 14 characters are index 1, the next 8 characters are index 2

n8i14

ignore the first 8 characters, and use the next 14 characters for index 1

If the tag contains a separator, then the numeric part can be replaced with '*' to mean 'read until the separator or end of tag', for example:

n*i*

ignore the left part of the tag until the separator, then use the second part

Starting from a coordinate sorted file, output paired reads to separate files, discarding singletons, supplementary and secondary reads. The resulting files can be used with, for example, the bwa aligner.

samtools collate -u -O in_pos.bam | \
samtools fastq -1 paired1.fq -2 paired2.fq -0 /dev/null -s /dev/null -n

Starting with a name collated file, output paired and singleton reads in a single file, discarding supplementary and secondary reads. To get all of the reads in a single file, it is necessary to redirect the output of samtools fastq. The output file is suitable for use with bwa mem -p which understands interleaved files containing a mixture of paired and singleton reads.

samtools fastq -0 /dev/null in_name.bam > all_reads.fq

Output paired reads in a single file, discarding supplementary and secondary reads. Save any singletons in a separate file. Append /1 and /2 to read names. This format is suitable for use by NextGenMap when using its -p and -q options. With this aligner, paired reads must be mapped separately to the singletons.

samtools fastq -0 /dev/null -s single.fq -N in_name.bam > paired.fq

• The way of specifying output files is far too complicated and easy to get wrong.

Written by Heng Li, with modifications by Martin Pollard and Jennifer Liddle, all from the Sanger Institute.

samtools(1), samtools-faidx(1), samtools-fqidx(1) samtools-import(1)

Samtools website: <http://www.htslib.org/>

samtools(1), samtools-faidx(1), samtools-fqidx(1), samtools-import(1).

The man page samtools-fastq(1) is an alias of samtools-fasta(1).