Package samtools

Tools for nucleotide sequence alignments in the SAM format

http://www.htslib.org/

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