samtools quickcheck [options] in.sam|in.bam|in.cram [ ... ] Quickly check that input files appear to be intact. Checks that beginning of the file cont

samtools view [options] in.sam|in.bam|in.cram [region...] With no options or regions specified, prints all alignments in the specified input alignment

samtools idxstats in.sam|in.bam|in.cram Retrieve and print stats in the index file corresponding to the input file. Before calling idxstats, the input

samtools cat [-b list] [-h header.sam] [-o out.bam] in1.bam in2.bam [ ... ] Concatenate BAMs or CRAMs. Although this works on either BAM or CRAM, all

samtools fastq [options] in.bam samtools fasta [options] in.bam Converts a BAM or CRAM into either FASTQ or FASTA format depending on the command invo

samtools bedcov [options] region.bed in1.sam|in1.bam|in1.cram[...] Reports the total read base count (i.e. the sum of per base read depths) for each g

Reads with a mapping quality below min-mapping-quality will be excluded

samtools depad [-SsCu1] [-T ref.fa] [-o output] in.bam Converts a BAM aligned against a padded reference to a BAM aligned against the depadded referen

Count alignments

samtools faidx <ref.fasta> [region1 [...]] Index reference sequence in the FASTA format or extract subsequence from indexed reference sequence. If no

samtools sort [-l level] [-m maxMem] [-o out.bam] [-O format] [-n] [-t tag] [-T tmpprefix] [-@ threads] [in.sam|in.bam|in.cram] Sort alignments by lef

convert sam to bam using samtools view

samtools calmd [-Eeubr] [-C capQcoef] aln.bam ref.fasta Generate the MD tag. If the MD tag is already present, this command will give a warning if the

samtools flagstat in.sam|in.bam|in.cram Does a full pass through the input file to calculate and print statistics to stdout. Provides counts for each

samtools collate [options] in.sam|in.bam|in.cram [<prefix>] Shuffles and groups reads together by their names. A faster alternative to a full query na

samtools fqidx <ref.fastq> [region1 [...]] Index reference sequence in the FASTQ format or extract subsequence from indexed reference sequence. If no

samtools addreplacerg [-r rg-line | -R rg-ID] [-m mode] [-l level] [-o out.bam] in.bam Adds or replaces read group tags in a file.

samtools merge [-nur1f] [-h inh.sam] [-t tag] [-R reg] [-b list] out.bam in1.bam [in2.bam in3.bam ... inN.bam] Merge multiple sorted alignment files,

Convert BAM to fastq

samtools depth [options] [in1.sam|in1.bam|in1.cram [in2.sam|in2.bam|in2.cram] [...]] Computes the read depth at each position or region.

samtools markdup [-l length] [-r] [-s] [-T] [-S] in.algsort.bam out.bam Mark duplicate alignments from a coordinate sorted file that has been run thro

This command identifies target regions by examining the continuity of read depth, computes haploid consensus sequences of targets and outputs a SAM wi

samtools split [options] merged.sam|merged.bam|merged.cram Splits a file by read group, producing one or more output files matching a common prefix (b

samtools dict ref.fasta|ref.fasta.gz Create a sequence dictionary file from a fasta file.

samtools fixmate [-rpcm] [-O format] in.nameSrt.bam out.bam Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment.

samtools reheader [-iP] in.header.sam in.bam Replace the header in in.bam with the header in in.header.sam. This command is much faster than replacing

samtools mpileup [-EB] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam [...]] Generate textual pileup for one o

samtools stats [options] in.sam|in.bam|in.cram [region...] samtools stats collects statistics from BAM files and outputs in a text format. The output

samtools fastq [options] in.bam samtools fasta [options] in.bam Converts a BAM or CRAM into either FASTQ or FASTA format depending on the command invo

samtools flags INT|STR[,...] Convert between textual and numeric flag representation. FLAGS: 0x1 PAIRED paired-end (or multiple-segment) sequencing te

samtools index [-bc] [-m INT] aln.bam|aln.cram [out.index] Index a coordinate-sorted BAM or CRAM file for fast random access. (Note that this does no

samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] in.bam Call and phase heterozygous SNPs.

samtools tview [-p chr:pos] [-s STR] [-d display] <in.sorted.bam> [ref.fasta] Text alignment viewer (based on the ncurses library). In the viewer, pre