Package samtools

Tools for nucleotide sequence alignments in the SAM format

SAM (Sequence Alignment/Map) is a flexible generic format for storing
nucleotide sequence alignment.
SAM Tools provide various utilities for manipulating alignments in the
SAM format, including sorting, merging, indexing and generating
alignments in a per-position format.

Version: 1.15.1

General Commands

samtools Utilities for the Sequence Alignment/Map (SAM) format
samtools-addreplacerg adds or replaces read group tags
samtools-ampliconclip clip reads using a BED file
samtools-ampliconstats produces statistics from amplicon sequencing alignment file
samtools-bedcov reports coverage over regions in a supplied BED file
samtools-calmd calculates MD and NM tags
samtools-cat concatenate files together
samtools-collate shuffles and groups reads together by their names
samtools-consensus produces produce a consensus FASTA/FASTQ/PILEUP
samtools-coverage produces a histogram or table of coverage per chromosome
samtools-depad convert padded BAM to unpadded BAM
samtools-depth computes the read depth at each position or region
samtools-dict create a sequence dictionary file from a fasta file
samtools-faidx indexes or queries regions from a fasta file
samtools-fasta converts a SAM/BAM/CRAM file to FASTA or FASTQ
samtools-fastq alias for samtools-fasta
samtools-fixmate fills in mate coordinates and insert size fields.
samtools-flags convert between textual and numeric flag representation.
samtools-flagstat counts the number of alignments for each FLAG type
samtools-fqidx Indexes or queries regions from a fastq file
samtools-head view SAM/BAM/CRAM file headers
samtools-idxstats reports alignment summary statistics
samtools-import converts FASTQ files to unmapped SAM/BAM/CRAM
samtools-index indexes SAM/BAM/CRAM files
samtools-markdup mark duplicate alignments in a coordinate sorted file
samtools-merge merges multiple sorted files into a single file
samtools-mpileup produces "pileup" textual format from an alignment
samtools-phase call and phase heterozygous SNPs
samtools-quickcheck a rapid sanity check on input files
samtools-reheader replaces the header in the input file
samtools-rmdup removes duplicate reads (obsolete)
samtools-samples prints the samples from an alignment file
samtools-sort sorts SAM/BAM/CRAM files
samtools-split splits a file by read group.
samtools-stats produces comprehensive statistics from alignment file
samtools-targetcut cut fosmid regions (for fosmid pool only)
samtools-tview display alignments in a curses-based interactive viewer.
samtools-view views and converts SAM/BAM/CRAM files
wgsim Whole-genome sequencing read simulator