📦 samtools

A

• ace2sam(1)ace to sam converter✨

S

• samtools(1)Utilities for the Sequence Alignment/Map (SAM) format✨
• 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-checksum(1)produces checksums of SAM / BAM / CRAM content✨
• samtools-collate(1)shuffles and groups reads together by their names✨
• samtools-consensus(1)produces a consensus FASTA/FASTQ/PILEUP✨
• samtools-coverage(1)produces a histogram or table of coverage per chromosome✨
• samtools-cram-size(1)list a break down of data types in a CRAM file✨
• 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-reset(1)removes the alignment information added by aligners and updates flags accordingly✨
• 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✨

W

• wgsim(1)Whole-genome sequencing read simulator✨