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.
samtools(1),
samtools-fasta(1),
samtools-fqidx(1),
samtools-fastq(1)
Samtools website: <
http://www.htslib.org/>