samtools-faidx - indexes or queries regions from a fasta file
samtools faidx ref.fasta [region1 [...]]
Index reference sequence in the FASTA format or extract
subsequence from indexed reference sequence. If no region is specified,
faidx will index the file and create <ref.fasta>.fai on
the disk. If regions are specified, the subsequences will be retrieved and
printed to stdout in the FASTA format.
The input file can be compressed in the BGZF format.
The sequences in the input file should all have different names.
If they do not, indexing will emit a warning about duplicate sequences and
retrieval will only produce subsequences from the first sequence with the
duplicated name.
FASTQ files can be read and indexed by this command. Without using
--fastq any extracted subsequence will be in FASTA format.
- -o, --output
FILE
- Write FASTA to file rather than to stdout.
- -n, --length
INT
- Length of FASTA sequence line. [60]
- -c, --continue
- Continue working if a non-existent region is requested.
- -r, --region-file
FILE
- Read regions from a file. Format is chr:from-to, one per line.
- -f, --fastq
- Read FASTQ files and output extracted sequences in FASTQ format. Same as
using samtools fqidx.
- -i,
--reverse-complement
- Output the sequence as the reverse complement. When this option is used,
“/rc” will be appended to the sequence names. To turn this
off or change the string appended, use the --mark-strand
option.
- --mark-strand
TYPE
- Append strand indicator to sequence name. TYPE can be one of:
- rc
- Append '/rc' when writing the reverse complement. This is the
default.
- no
- Do not append anything.
- sign
- Append '(+)' for forward strand or '(-)' for reverse complement. This
matches the output of “bedtools getfasta -s”.
- custom,<pos>,<neg>
- Append string <pos> to names when writing the forward strand and
<neg> when writing the reverse strand. Spaces are preserved, so it
is possible to move the indicator into the comment part of the description
line by including a leading space in the strings <pos> and
<neg>.
- --fai-idx
FILE
- Read/Write to specified index file.
- --gzi-idx
FILE
- Read/Write to specified compressed file index (used with .gz files).
- -h, --help
- Print help message and exit.
Written by Heng Li, with modifications by Andrew Whitwham and
Robert Davies, all from the Sanger Institute.