Samtools is a suite of programs for interacting with high-throughput
sequencing data. It consists of three separate repositories:
- Samtools
- Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
- BCFtools
- Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP
and short indel sequence variants
- HTSlib
- A C library for reading/writing high-throughput sequencing data
Samtools and BCFtools both use HTSlib internally, but these source packages
contain their own copies of htslib so they can be built independently.
Location and version:
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$ which samtools
/local/cluster/bin/samtools
$ samtools version
samtools 1.14
Using htslib 1.14
Copyright (C) 2021 Genome Research Ltd.
Samtools compilation details:
Features: build=configure curses=yes
CC: gcc
CPPFLAGS:
CFLAGS: -Wall -g -O2
LDFLAGS:
HTSDIR: htslib-1.14
LIBS:
CURSES_LIB: -lncursesw
HTSlib compilation details:
Features: build=configure plugins=no libcurl=yes S3=yes GCS=yes libdeflate=no lzma=yes bzip2=yes htscodecs=1.1.1-1-ged325d7
CC: gcc
CPPFLAGS:
CFLAGS: -Wall -g -O2 -fvisibility=hidden
LDFLAGS: -fvisibility=hidden
HTSlib URL scheme handlers present:
built-in: preload, data, file
S3 Multipart Upload: s3w, s3w+https, s3w+http
Amazon S3: s3+https, s3+http, s3
Google Cloud Storage: gs+http, gs+https, gs
libcurl: imaps, pop3, http, gopher, sftp, ftps, imap, smtp, smtps, rtsp, scp, ftp, telnet, ldap, https, ldaps, tftp, pop3s, dict
crypt4gh-needed: crypt4gh
mem: mem
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help message:
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$ samtools help
Program: samtools (Tools for alignments in the SAM format)
Version: 1.14 (using htslib 1.14)
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
ampliconclip clip oligos from the end of reads
-- 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
import Converts FASTA or FASTQ files to SAM/BAM/CRAM
-- 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)
ampliconstats generate amplicon specific stats
-- Viewing
flags explain BAM flags
tview text alignment viewer
view SAM<->BAM<->CRAM conversion
depad convert padded BAM to unpadded BAM
samples list the samples in a set of SAM/BAM/CRAM files
-- Misc
help [cmd] display this help message or help for [cmd]
version detailed version information
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software ref: https://github.com/samtools/samtools
research ref: https://doi.org/10.1093/gigascience/giab008