$ samtools
Program: samtools (Tools for alignments in the SAM format)
Version: 1.10 (using htslib 1.10)
Usage: samtools <command> [options]
Commands:
-- Indexing
dict create a sequence dictionary file
faidx index/extract FASTA
fqidx index/extract FASTQ
index index alignment
-- Editing
calmd recalculate MD/NM tags and '=' bases
fixmate fix mate information
reheader replace BAM header
targetcut cut fosmid regions (for fosmid pool only)
addreplacerg adds or replaces RG tags
markdup mark duplicates
-- File operations
collate shuffle and group alignments by name
cat concatenate BAMs
merge merge sorted alignments
mpileup multi-way pileup
sort sort alignment file
split splits a file by read group
quickcheck quickly check if SAM/BAM/CRAM file appears intact
fastq converts a BAM to a FASTQ
fasta converts a BAM to a FASTA
-- Statistics
bedcov read depth per BED region
coverage alignment depth and percent coverage
depth compute the depth
flagstat simple stats
idxstats BAM index stats
phase phase heterozygotes
stats generate stats (former bamcheck)
-- Viewing
flags explain BAM flags
tview text alignment viewer
view SAM<->BAM<->CRAM conversion
depad convert padded BAM to unpadded BAM
View
$ samtools view
Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]
Options:
-b output BAM
-C output CRAM (requires -T)
-1 use fast BAM compression (implies -b)
-u uncompressed BAM output (implies -b)
-h include header in SAM output
-H print SAM header only (no alignments)
-c print only the count of matching records
-o FILE output file name [stdout]
-U FILE output reads not selected by filters to FILE [null]
-t FILE FILE listing reference names and lengths (see long help) [null]
-X include customized index file
-L FILE only include reads overlapping this BED FILE [null]
-r STR only include reads in read group STR [null]
-R FILE only include reads with read group listed in FILE [null]
-d STR:STR
only include reads with tag STR and associated value STR [null]
-D STR:FILE
only include reads with tag STR and associated values listed in
FILE [null]
-q INT only include reads with mapping quality >= INT [0]
-l STR only include reads in library STR [null]
-m INT only include reads with number of CIGAR operations consuming
query sequence >= INT [0]
-f INT only include reads with all of the FLAGs in INT present [0]
-F INT only include reads with none of the FLAGS in INT present [0]
-G INT only EXCLUDE reads with all of the FLAGs in INT present [0]
-s FLOAT subsample reads (given INT.FRAC option value, 0.FRAC is the
fraction of templates/read pairs to keep; INT part sets seed)
-M use the multi-region iterator (increases the speed, removes
duplicates and outputs the reads as they are ordered in the file)
-x STR read tag to strip (repeatable) [null]
-B collapse the backward CIGAR operation
-? print long help, including note about region specification
-S ignored (input format is auto-detected)
--no-PG do not add a PG line
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
-T, --reference FILE
Reference sequence FASTA FILE [null]
-@, --threads INT
Number of additional threads to use [0]
--write-index
Automatically index the output files [off]
--verbosity INT
Set level of verbosity
Sort
$ samtools sort
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set)
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
--no-PG do not add a PG line
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
-@, --threads INT
Number of additional threads to use [0]
--verbosity INT
Set level of verbosity
Index
$ samtools index
Usage: samtools index [-bc] [-m INT] <in.bam> [out.index]
Options:
-b Generate BAI-format index for BAM files [default]
-c Generate CSI-format index for BAM files
-m INT Set minimum interval size for CSI indices to 2^INT [14]
-@ INT Sets the number of threads [none]
Depth
$ samtools depth
Usage: samtools depth [options] in1.bam [in2.bam [...]]
Options:
-a output all positions (including zero depth)
-a -a (or -aa) output absolutely all positions, including unused ref. sequences
-b <bed> list of positions or regions
-X use customized index files
-f <list> list of input BAM filenames, one per line [null]
-H print a file header
-l <int> read length threshold (ignore reads shorter than <int>) [0]
-d/-m <int> maximum coverage depth [8000]. If 0, depth is set to the maximum
integer value, effectively removing any depth limit.
-o FILE where to write output to [stdout]
-q <int> base quality threshold [0]
-Q <int> mapping quality threshold [0]
-r <chr:from-to> region
-g <flags> include reads that have any of the specified flags set [0]
-G <flags> filter out reads that have any of the specified flags set [UNMAP,SECONDARY,QCFAIL,DUP]
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
--verbosity INT
Set level of verbosity
The output is a simple tab-separated table with three columns: reference name,
position, and coverage depth. Note that positions with zero coverage may be
omitted by default; see the -a option.