Samtools
- ace2sam(1) ace to sam converter
- samtools-addreplacerg(1) adds or replaces read group tags
- samtools-ampliconclip(1) clip reads using a BED file
- samtools-ampliconstats(1) produces statistics from amplicon sequencing alignment file
- samtools-bedcov(1) reports coverage over regions in a supplied BED file
- samtools-calmd(1) calculates MD and NM tags
- samtools-cat(1) concatenate files together
- samtools-collate(1) shuffles and groups reads together by their names
- samtools-consensus(1) produces produce a consensus FASTA/FASTQ/PILEUP
- samtools-coverage(1) produces a histogram or table of coverage per chromosome
- samtools-depad(1) convert padded BAM to unpadded BAM
- samtools-depth(1) computes the read depth at each position or region
- samtools-dict(1) create a sequence dictionary file from a fasta file
- samtools-faidx(1) indexes or queries regions from a fasta file
- samtools-fasta(1) converts a SAM/BAM/CRAM file to FASTA or FASTQ
- samtools-fastq(1) converts a SAM/BAM/CRAM file to FASTA or FASTQ
- samtools-fixmate(1) fills in mate coordinates and insert size fields.
- samtools-flags(1) convert between textual and numeric flag representation.
- samtools-flagstat(1) counts the number of alignments for each FLAG type
- samtools-fqidx(1) Indexes or queries regions from a fastq file
- samtools-head(1) view SAM/BAM/CRAM file headers
- samtools-idxstats(1) reports alignment summary statistics
- samtools-import(1) converts FASTQ files to unmapped SAM/BAM/CRAM
- samtools-index(1) indexes SAM/BAM/CRAM files
- samtools-markdup(1) mark duplicate alignments in a coordinate sorted file
- samtools-merge(1) merges multiple sorted files into a single file
- samtools-mpileup(1) produces "pileup" textual format from an alignment
- samtools-phase(1) call and phase heterozygous SNPs
- samtools-quickcheck(1) a rapid sanity check on input files
- samtools-reference(1) extracts an embedded reference from a CRAM file
- samtools-reheader(1) replaces the header in the input file
- samtools-rmdup(1) removes duplicate reads (obsolete)
- samtools-samples(1) prints the samples from an alignment file
- samtools-sort(1) sorts SAM/BAM/CRAM files
- samtools-split(1) splits a file by read group.
- samtools-stats(1) produces comprehensive statistics from alignment file
- samtools-targetcut(1) cut fosmid regions (for fosmid pool only)
- samtools-tview(1) display alignments in a curses-based interactive viewer.
- samtools-view(1) views and converts SAM/BAM/CRAM files
- samtools.pl(1) helper script for SAMtools
- samtools(1) Utilities for the Sequence Alignment/Map (SAM) format
- wgsim(1) short read simulator