Provided by: samtools_1.16.1-1_amd64 bug


       samtools - Utilities for the Sequence Alignment/Map (SAM) format


       samtools addreplacerg -r 'ID:fish' -r 'LB:1334' -r 'SM:alpha' -o output.bam input.bam

       samtools ampliconclip -b bed.file input.bam

       samtools ampliconstats primers.bed in.bam

       samtools bedcov aln.sorted.bam

       samtools calmd in.sorted.bam ref.fasta

       samtools cat out.bam in1.bam in2.bam in3.bam

       samtools collate -o aln.name_collated.bam aln.sorted.bam

       samtools consensus -o out.fasta in.bam

       samtools coverage aln.sorted.bam

       samtools depad input.bam

       samtools depth aln.sorted.bam

       samtools dict -a GRCh38 -s "Homo sapiens" ref.fasta

       samtools faidx ref.fasta

       samtools fasta input.bam > output.fasta

       samtools fastq input.bam > output.fastq

       samtools fixmate in.namesorted.sam out.bam

       samtools flags PAIRED,UNMAP,MUNMAP

       samtools flagstat aln.sorted.bam

       samtools fqidx ref.fastq

       samtools head in.bam

       samtools idxstats aln.sorted.bam

       samtools import input.fastq > output.bam

       samtools index aln.sorted.bam

       samtools markdup in.algnsorted.bam out.bam

       samtools merge out.bam in1.bam in2.bam in3.bam

       samtools mpileup -C50 -f ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam

       samtools phase input.bam

       samtools quickcheck in1.bam in2.cram

       samtools reference -o ref.fa in.cram

       samtools reheader in.header.sam in.bam > out.bam

       samtools samples input.bam

       samtools sort -T /tmp/aln.sorted -o aln.sorted.bam aln.bam

       samtools split merged.bam

       samtools stats aln.sorted.bam

       samtools targetcut input.bam

       samtools tview aln.sorted.bam ref.fasta

       samtools view -bt ref_list.txt -o aln.bam aln.sam.gz


       Samtools  is  a  set  of  utilities  that  manipulate  alignments  in  the  SAM  (Sequence
       Alignment/Map), BAM, and CRAM formats.  It converts between  the  formats,  does  sorting,
       merging and indexing, and can retrieve reads in any regions swiftly.

       Samtools  is  designed  to  work on a stream. It regards an input file `-' as the standard
       input (stdin) and an output file `-' as the standard output (stdout). Several commands can
       thus be combined with Unix pipes. Samtools always output warning and error messages to the
       standard error output (stderr).

       Samtools is also able to open files on remote FTP or HTTP(S)  servers  if  the  file  name
       starts  with  `ftp://', `http://', etc.  Samtools checks the current working directory for
       the index file and will download the index upon absence. Samtools does  not  retrieve  the
       entire alignment file unless it is asked to do so.

       If  an  index is needed, samtools looks for the index suffix appended to the filename, and
       if that isn't found it tries again without the filename  suffix  (for  example  in.bam.bai
       followed  by  in.bai).  However if an index is in a completely different location or has a
       different name, both the main data filename and index filename can be pasted together with
       ##idx##.   For  example  /data/in.bam##idx##/indices/in.bam.bai  may be used to explicitly
       indicate where the data and index files reside.


       Each command has its own man page which can be viewed using e.g. man samtools-view or with
       a  recent  GNU  man  using man samtools view.  Below we have a brief summary of syntax and
       sub-command description.

       Options common to all sub-commands are documented below  in  the  GLOBAL  COMMAND  OPTIONS

       view      samtools view [options] in.sam|in.bam|in.cram [region...]

                 With  no  options  or  regions specified, prints all alignments in the specified
                 input alignment file (in SAM, BAM, or CRAM format) to  standard  output  in  SAM
                 format (with no header by default).

                 You  may  specify  one  or  more space-separated region specifications after the
                 input filename to restrict output to only those  alignments  which  overlap  the
                 specified  region(s).  Use of region specifications requires a coordinate-sorted
                 and indexed input file.

                 Options exist to change the output format from SAM  to  BAM  or  CRAM,  so  this
                 command also acts as a file format conversion utility.

       tview     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, press `?'
                 for help and press `g' to check the alignment start from a region in the  format
                 like  `chr10:10,000,000'  or  `=10,000,000'  when  viewing  the  same  reference

                 samtools quickcheck [options] in.sam|in.bam|in.cram [ ... ]

                 Quickly check that input files appear to be intact. Checks that beginning of the
                 file  contains  a  valid  header  (all  formats)  containing at least one target
                 sequence and then seeks to the end of the file and checks  that  an  end-of-file
                 (EOF) is present and intact (BAM only).

                 Data  in  the  middle of the file is not read since that would be much more time
                 consuming, so please note that this command will not detect internal corruption,
                 but  is  useful  for testing that files are not truncated before performing more
                 intensive tasks on them.

                 This command will exit with a non-zero exit code if any input files don't have a
                 valid  header  or  are missing an EOF block. Otherwise it will exit successfully
                 (with a zero exit code).

       head      samtools head [options] in.sam|in.bam|in.cram

                 Prints the input file's headers and optionally  also  its  first  few  alignment
                 records. This command always displays the headers as they are in the file, never
                 adding an extra @PG header itself.

       index     samtools index [-bc] [-m INT] aln.sam.gz|aln.bam|aln.cram [out.index]

                 Index a coordinate-sorted SAM, BAM or CRAM file for fast  random  access.   Note
                 for  SAM  this only works if the file has been BGZF compressed first.  (Starting
                 from Samtools 1.16, this command can also be given several alignment  filenames,
                 which are indexed individually.)

                 This  index  is needed when region arguments are used to limit samtools view and
                 similar commands to particular regions of interest.

                 If an output filename is given, the index file will  be  written  to  out.index.
                 Otherwise,  for  a CRAM file aln.cram, index file aln.cram.crai will be created;
                 for a BAM or SAM  file  aln.bam,  either  aln.bam.bai  or  aln.bam.csi  will  be
                 created, depending on the index format selected.

       sort      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 leftmost coordinates, or by read name when -n  is  used.   An
                 appropriate  @HD-SO  sort  order  header  tag  will  be added or an existing one
                 updated if necessary.

                 The sorted output is written to standard output by default, or to the  specified
                 file  (out.bam)  when -o is used.  This command will also create temporary files
                 tmpprefix.%d.bam as needed when the entire alignment data cannot fit into memory
                 (as controlled via the -m option).

                 Consider using samtools collate instead if you need name collated data without a
                 full lexicographical sort.

                 Note that if the sorted output file is to be indexed with  samtools  index,  the
                 default  coordinate  sort  must  be  used.   Thus  the  -n  and  -t  options are
                 incompatible with samtools index.

       collate   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  name  sort, collate ensures that reads of the same name are grouped
                 together in contiguous groups, but doesn't make any guarantees about  the  order
                 of read names between groups.

                 The  output from this command should be suitable for any operation that requires
                 all reads from the same template to be grouped together.

       idxstats  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 BAM file should be indexed by samtools index.

                 If  run  on a SAM or CRAM file or an unindexed BAM file, this command will still
                 produce the same summary statistics, but does so by reading through  the  entire
                 file.  This is far slower than using the BAM indices.

                 The  output  is  TAB-delimited  with  each line consisting of reference sequence
                 name, sequence length, # mapped reads and # unmapped reads.  It  is  written  to

       flagstat  samtools flagstat in.sam|in.bam|in.cram

                 Does  a  full  pass  through the input file to calculate and print statistics to

                 Provides counts for each of 13 categories based primarily on bit  flags  in  the
                 FLAG field. Each category in the output is broken down into QC pass and QC fail,
                 which is presented as "#PASS + #FAIL" followed by a description of the category.

       flags     samtools flags INT|STR[,...]

                 Convert between textual and numeric flag representation.


                   0x1   PAIRED          paired-end (or multiple-segment) sequencing technology
                   0x2   PROPER_PAIR     each segment properly aligned according to the aligner
                   0x4   UNMAP           segment unmapped
                   0x8   MUNMAP          next segment in the template unmapped
                  0x10   REVERSE         SEQ is reverse complemented
                  0x20   MREVERSE        SEQ of the next segment in the template is reverse complemented
                  0x40   READ1           the first segment in the template
                  0x80   READ2           the last segment in the template
                 0x100   SECONDARY       secondary alignment
                 0x200   QCFAIL          not passing quality controls
                 0x400   DUP             PCR or optical duplicate
                 0x800   SUPPLEMENTARY   supplementary alignment

       stats     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 can be visualized graphically using plot-bamstats.

       bedcov    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 genomic region specified in the supplied BED file. The regions  are  output
                 as  they appear in the BED file and are 0-based.  Counts for each alignment file
                 supplied are reported in separate columns.

       depth     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 ampliconstats [options] primers.bed in.sam|in.bam|in.cram[...]

                 samtools  ampliconstats  collects  statistics  from  one or more input alignment
                 files and produces  tables  in  text  format.   The  output  can  be  visualized
                 graphically using plot-ampliconstats.

                 The  alignment files should have previously been clipped of primer sequence, for
                 example by samtools ampliconclip and  the  sites  of  these  primers  should  be
                 specified as a bed file in the arguments.

       mpileup   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 or multiple BAM files.  For VCF and BCF  output,
                 please  use the bcftools mpileup command instead.  Alignment records are grouped
                 by sample (SM) identifiers in @RG  header  lines.   If  sample  identifiers  are
                 absent, each input file is regarded as one sample.

                 See  the  samtools-mpileup  man  page for a description of the pileup format and

       consensus samtools consensus [options] in.bam

                 Generate consensus from a SAM, BAM or CRAM file based on  the  contents  of  the
                 alignment records.  The consensus is written either as FASTA, FASTQ, or a pileup
                 oriented format.

                 The default output for FASTA and FASTQ formats  include  one  base  per  non-gap
                 consensus.   Hence  insertions  with  respect  to  the aligned reference will be
                 included and deletions removed.  This behaviour can be adjusted.

                 Two  consensus  calling  algorithms  are  offered.   The  default   computes   a
                 heterozygous  consensus  in a Bayesian manner, derived from the "Gap5" consensus
                 algorithm.  A simpler base frequency counting method is also available.

       reference samtools reference [options] in.bam

                 Generate a reference from a SAM, BAM or CRAM file based on the contents  of  the
                 SEQuence  field  and  the  MD:Z:  auxiliary tags, or from the embedded reference
                 blocks within a CRAM file (provided it was  constructed  using  the  embed_ref=1

       coverage  samtools coverage [options] [in1.sam|in1.bam|in1.cram [in2.sam|in2.bam|in2.cram]

                 Produces a histogram or table of coverage per chromosome.

       merge     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, producing a single sorted output file
                 that contains all the input records and maintains the existing sort order.

                 If -h is specified the @SQ headers of  input  files  will  be  merged  into  the
                 specified  header, otherwise they will be merged into a composite header created
                 from the input headers.  If the @SQ headers differ in order this may require the
                 output file to be re-sorted after merge.

                 The  ordering  of  the records in the input files must match the usage of the -n
                 and -t command-line  options.   If  they  do  not,  the  output  order  will  be
                 undefined.  See sort for information about record ordering.

       split     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 (by default based on the input filename) each containing one read-

       cat       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 input
                 files must be the same format as each other. The  sequence  dictionary  of  each
                 input  file  must  be identical, although this command does not check this. This
                 command uses a similar trick to reheader which enables fast BAM concatenation.

       import    samtools import [options] in.fastq [ ... ]

                 Converts one or more FASTQ files to unaligned SAM, BAM or CRAM.   These  formats
                 offer  a  richer  capability of tracking sample meta-data via the SAM header and
                 per-read meta-data via the auxiliary tags.  The fastq command  may  be  used  to
                 reverse this conversion.

       fastq/a   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 invoked. The files will be automatically compressed if  the  file  names
                 have a .gz or .bgzf extension.

                 The  input  to  this  program must be collated by name.  Use samtools collate or
                 samtools sort -n to ensure this.

       faidx     samtools faidx <ref.fasta> [region1 [...]]

                 Index reference sequence in the FASTA format or extract subsequence from indexed
                 reference  sequence.  If  no  region is specified, faidx will index the file and
                 create <ref.fasta>.fai on the disk. If regions are specified,  the  subsequences
                 will be retrieved and printed to stdout in the FASTA format.

                 The input file can be compressed in the BGZF format.

                 FASTQ  files can be read and indexed by this command.  Without using --fastq any
                 extracted subsequence will be in FASTA format.

       fqidx     samtools fqidx <ref.fastq> [region1 [...]]

                 Index reference sequence in the FASTQ format or extract subsequence from indexed
                 reference  sequence.  If  no  region is specified, fqidx will index the file and
                 create <ref.fastq>.fai on the disk. If regions are specified,  the  subsequences
                 will be retrieved and printed to stdout in the FASTQ format.

                 The input file can be compressed in the BGZF format.

                 samtools  fqidx  should  only  be  used  on  fastq  files with a small number of
                 entries.  Trying to use it on a file containing  millions  of  short  sequencing
                 reads  will  produce  an  index  that is almost as big as the original file, and
                 searches using the index will be very slow and use a lot of memory.

       dict      samtools dict ref.fasta|ref.fasta.gz

                 Create a sequence dictionary file from a fasta file.

       calmd     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 MD tag generated is different from the existing tag. Output SAM
                 by default.

                 Calmd can also read and write CRAM files although in most cases it is  pointless
                 as  CRAM recalculates MD and NM tags on the fly.  The one exception to this case
                 is where both input and output CRAM files have been / are being created with the
                 no_ref option.

       fixmate   samtools fixmate [-rpcm] [-O format] in.nameSrt.bam out.bam

                 Fill  in  mate  coordinates,  ISIZE  and  mate  related flags from a name-sorted

       markdup   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
                 through  samtools fixmate with the -m option.  This program relies on the MC and
                 ms tags that fixmate provides.

       rmdup     samtools rmdup [-sS] <> <out.bam>

                 This command is obsolete. Use markdup instead.

                 samtools addreplacerg [-r rg-line | -R rg-ID] [-m mode] [-l level] [-o  out.bam]

                 Adds or replaces read group tags in a file.

       reheader  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 the header with a BAM→SAM→BAM conversion.

                 By default this command  outputs  the  BAM  or  CRAM  file  to  standard  output
                 (stdout),  but  for  CRAM  format files it has the option to perform an in-place
                 edit, both reading and writing to  the  same  file.   No  validity  checking  is
                 performed  on  the header, nor that it is suitable to use with the sequence data

       targetcut samtools targetcut [-Q minBaseQ] [-i inPenalty] [-0 em0] [-1 em1] [-2  em2]  [-f
                 ref] in.bam

                 This  command  identifies  target  regions  by  examining the continuity of read
                 depth, computes haploid consensus sequences of targets and outputs  a  SAM  with
                 each  sequence  corresponding to a target. When option -f is in use, BAQ will be
                 applied. This command is only designed for cutting  fosmid  clones  from  fosmid
                 pool sequencing [Ref. Kitzman et al. (2010)].

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

                 Call and phase heterozygous SNPs.

       depad     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 reference.  The padded reference may contain verbatim "*" bases in  it,
                 but  "*"  bases  are also counted in the reference numbering.  This means that a
                 sequence base-call aligned against a reference "*" is considered to be  a  cigar
                 match  ("M"  or "X") operator (if the base-call is "A", "C", "G" or "T").  After
                 depadding the reference "*" bases are deleted and such  aligned  sequence  base-
                 calls  become  insertions.   Similarly  transformations  apply for deletions and
                 padding cigar operations.

                 samtools ampliconclip [-o out.file] [-f stat.file]  [--soft-clip]  [--hard-clip]
                 [--both-ends] [--strand] [--clipped] [--fail] [--no-PG] -b bed.file in.file

                 Clip reads in a SAM compatible file based on data from a BED file.

       samples   samtools samples [-o out.file] [-i] [-T TAG] [-f refs.fasta] [-F refs_list] [-X]

                 Prints the samples from alignment files


       These  are  options  that are passed after the samtools command, before any sub-command is

       help, --help
              Display a brief usage message listing the samtools commands available.  If the name
              of  a  command  is also given, e.g., samtools help view, the detailed usage message
              for that particular command is displayed.

              Display the  version  numbers  and  copyright  information  for  samtools  and  the
              important libraries used by samtools.

              Display the full samtools version number in a machine-readable format.


       Several  long-options  are  shared  between  multiple  samtools sub-commands: --input-fmt,
       --input-fmt-option, --output-fmt,  --output-fmt-option,  --reference,  --write-index,  and
       --verbosity.   The  input  format  is  typically auto-detected so specifying the format is
       usually unnecessary and the option is  included  for  completeness.   Note  that  not  all
       subcommands have all options.  Consult the subcommand help for more details.

       Format  strings recognised are "sam", "sam.gz", "bam" and "cram".  They may be followed by
       a comma separated list of options as key or key=value. See below for examples.

       The fmt-option arguments accept either a single option or option=value.   Note  that  some
       options  only  work  on  some file formats and only on read or write streams.  If value is
       unspecified for a boolean option, the value is assumed to be 1.  The valid options are  as

           Output  only.  Specifies the compression level from 1 to 9, or 0 for uncompressed.  If
           the output format is SAM, this also enables BGZF compression, otherwise  SAM  defaults
           to uncompressed.

           Specifies  the number of threads to use during encoding and/or decoding.  For BAM this
           will be encoding only.  In CRAM the threads are dynamically shared between encoder and

           Apply  filter  STRING  to  all incoming records, rejecting any that do not satisfy the
           expression.  See the FILTER EXPRESSIONS section below for specifics.

           Specifies a FASTA reference file for use in CRAM encoding or decoding.  It usually  is
           not  required for decoding except in the situation of the MD5 not being obtainable via
           the REF_PATH or REF_CACHE environment variables.

           CRAM input only; defaults to 1 (on).  CRAM does not typically store MD  and  NM  tags,
           preferring  to  generate  them  on the fly.  When this option is 0 missing MD, NM tags
           will not be generated.  It can be  particularly  useful  when  combined  with  a  file
           encoded using store_md=1 and store_nm=1.

           CRAM  output  only;  defaults  to 0 (off).  CRAM normally only stores MD tags when the
           reference is unknown and lets  the  decoder  generate  these  values  on-the-fly  (see

           CRAM  output  only;  defaults  to 0 (off).  CRAM normally only stores NM tags when the
           reference is unknown and lets  the  decoder  generate  these  values  on-the-fly  (see

           CRAM  input  only;  defaults  to  0  (off).   When enabled, md5 checksum errors on the
           reference sequence and block checksum errors within CRAM are  ignored.   Use  of  this
           option is strongly discouraged.

           CRAM  input  only;  specifies  which SAM columns need to be populated.  By default all
           fields are used.  Limiting  the  decode  to  specific  columns  can  have  significant
           performance  gains.  The bit-field is a numerical value constructed from the following

              0x1   SAM_QNAME
              0x2   SAM_FLAG
              0x4   SAM_RNAME
              0x8   SAM_POS
             0x10   SAM_MAPQ
             0x20   SAM_CIGAR
             0x40   SAM_RNEXT
             0x80   SAM_PNEXT
            0x100   SAM_TLEN
            0x200   SAM_SEQ
            0x400   SAM_QUAL
            0x800   SAM_AUX
           0x1000   SAM_RGAUX

           CRAM input only; defaults to output filename.  Any sequences with auto-generated  read
           names will use string as the name prefix.

           CRAM  output  only;  defaults to 0 (off).  By default CRAM generates one container per
           reference sequence, except in the case of many small references (such as a  fragmented

           CRAM output only.  Specifies the CRAM version number.  Acceptable values are "2.1" and

           CRAM output only; defaults to 10000.

           CRAM output only; defaults to 1.  The effect of having multiple slices  per  container
           is to share the compression header block between multiple slices.  This is unlikely to
           have any significant impact unless the number  of  sequences  per  slice  is  reduced.
           (Together these two options control the granularity of random access.)

           CRAM  output  only;  defaults  to  0  (off).   If  1,  this will store portions of the
           reference sequence in each  slice,  permitting  decode  without  having  requiring  an
           external copy of the reference sequence.

           CRAM  output  only; defaults to 0 (off).  If 1, sequences will be stored verbatim with
           no reference encoding.  This can be useful if no reference is available for the file.

           CRAM output  only;  defaults  to  0  (off).   Permits  use  of  bzip2  in  CRAM  block

           CRAM output only; defaults to 0 (off).  Permits use of lzma in CRAM block compression.

           CRAM  ≥  3.1 output only; enables and disables the fqzcomp quality compression method.
           This is on by default for version 3.1 and  above  only  when  the  small  and  archive
           profiles are in use.

           CRAM  ≥  3.1 output only; enables and disables the namne tokeniser compression method.
           This is on by default for version 3.1 and above.

           CRAM output only; defaults to 0 (off).  If 1, templates with all  members  within  the
           same  CRAM  slice will have their read names removed.  New names will be automatically
           generated during decoding.  Also see the name_prefix option.

       fast, normal, small, archive
           CRAM output only.  Set the CRAM compression profile.  This  is  a  simplified  way  of
           setting  many  output  options at once.  It changes the following options according to
           the profile in use.  The "normal" profile is the default.

           Option           fast    normal   small   archive
           level            1       5        6       7
           use_bzip2        off     off      on      on
           use_lzma         off     off      off     on if level>7
           use_tok(*)       off     on       on      on
           use_fqz(*)       off     off      on      on
           use_arith(*)     off     off      off     on
           seqs_per_slice   10000   10000    25000   100000

           (*) use_tok, use_fqz and use_arith are only enabled for CRAM version 3.1 and above.

           The level listed is only the default value, and  will  not  be  set  if  it  has  been
           explicitly changed already.  Additionally bases_per_slice is set to 500*seqs_per_slice
           unless previously explicitly set.

       For example:

           samtools view --input-fmt-option decode_md=0
               --output-fmt cram,version=3.0 --output-fmt-option embed_ref
               --output-fmt-option seqs_per_slice=2000 -o foo.cram foo.bam

           samtools view -O cram,small -o bar.cram bar.bam

       The --write-index option enables automatic index creation while writing out BAM,  CRAM  or
       bgzf  SAM  files.   Note  to  get compressed SAM as the output format you need to manually
       request a compression level, otherwise all SAM files are uncompressed.  By default SAM and
       BAM  will  use  CSI  indices  while CRAM will use CRAI indices.  If you need to create BAI
       indices note that it is possible to specify the name of the index being  written  to,  and
       hence the format, by using the filename##idx##indexname notation.

       For example: to convert a BAM to a compressed SAM with CSI indexing:

           samtools view -h -O sam,level=6 --write-index in.bam -o out.sam.gz

       To convert a SAM to a compressed BAM using BAI indexing:

           samtools view --write-index in.sam -o out.bam##idx##out.bam.bai

       The  --verbosity INT option sets the verbosity level for samtools and HTSlib.  The default
       is 3 (HTS_LOG_WARNING); 2 reduces warning messages and 0 or  1  also  reduces  some  error
       messages,  while  values  greater than 3 produce increasing numbers of additional warnings
       and logging messages.


       The CRAM format requires use of a reference sequence for both reading and writing.

       When reading a CRAM the @SQ headers are interrogated to identify  the  reference  sequence
       MD5sum  (M5:  tag) and the local reference sequence filename (UR: tag).  Note that http://
       and ftp:// based URLs in the UR: field are not used, but local fasta  filenames  (with  or
       without file://) can be used.

       To  create  a  CRAM the @SQ headers will also be read to identify the reference sequences,
       but M5: and UR: tags may not be present. In this case the -T and -t  options  of  samtools
       view  may  be  used to specify the fasta or fasta.fai filenames respectively (provided the
       .fasta.fai file is also backed up by a .fasta file).

       The search order to obtain a reference is:

       1. Use any local file specified by the command line options (eg -T).

       2. Look for MD5 via REF_CACHE environment variable.

       3. Look for MD5 in each element of the REF_PATH environment variable.

       4. Look for a local file listed in the UR: header tag.


       Filter expressions are used as an  on-the-fly  checking  of  incoming  SAM,  BAM  or  CRAM
       records, discarding records that do not match the specified expression.

       The language used is primarily C style, but with a few differences in the precedence rules
       for bit operators and the inclusion of regular expression matching.

       The operator precedence, from strongest binding to weakest, is:

       Grouping        (, )             E.g. "(1+2)*3"
       Values:         literals, vars   Numbers, strings and variables
       Unary ops:      +, -, !, ~       E.g. -10 +10, !10 (not), ~5 (bit not)
       Math ops:       *, /, %          Multiply, division and (integer) modulo

       Math ops:       +, -             Addition / subtraction
       Bit-wise:       &                Integer AND
       Bit-wise        ^                Integer XOR
       Bit-wise        |                Integer OR
       Conditionals:   >, >=, <, <=
       Equality:       ==, !=, =~, !~   =~ and !~ match regular expressions
       Boolean:        &&, ||           Logical AND / OR

       Expressions are computed using floating point mathematics, so "10 / 4"  evaluates  to  2.5
       rather  than  2.  They may be written as integers in decimal or "0x" plus hexadecimal, and
       floating point with or without exponents.However operations that require integers first do
       an  implicit  type conversion, so "7.9 % 5" is 2 and "7.9 & 4.1" is equivalent to "7 & 4",
       which is 4.  Strings are always specified using double quotes.  To get a double quote in a
       string,  use  backslash.  Similarly a double backslash is used to get a literal backslash.
       For example ab\"c\\d is the string ab"c\d.

       Comparison operators are evaluated as a match being 1 and a mismatch being 0, thus  "(2  >
       1)  +  (3  <  5)"  evaluates  as 2.  All comparisons involving undefined (null) values are
       deemed to be false.

       The variables are where the file format specifics are accessed from the  expression.   The
       variables  correspond  to  SAM  fields,  for  example  to find paired alignments with high
       mapping quality and a very large insert size, we may use the expression  "mapq  >=  30  &&
       (tlen >= 100000 || tlen <= -100000)".  Valid variable names and their data types are:

       endpos               int            Alignment end position (1-based)
       flag                 int            Combined FLAG field
       flag.paired          int            Single bit, 0 or 1
       flag.proper_pair     int            Single bit, 0 or 2
       flag.unmap           int            Single bit, 0 or 4
       flag.munmap          int            Single bit, 0 or 8
       flag.reverse         int            Single bit, 0 or 16
       flag.mreverse        int            Single bit, 0 or 32
       flag.read1           int            Single bit, 0 or 64
       flag.read2           int            Single bit, 0 or 128
       flag.secondary       int            Single bit, 0 or 256
       flag.qcfail          int            Single bit, 0 or 512
       flag.dup             int            Single bit, 0 or 1024
       flag.supplementary   int            Single bit, 0 or 2048
       library              string         Library (LB header via RG)
       mapq                 int            Mapping quality
       mpos                 int            Synonym for pnext
       mrefid               int            Mate reference number (0 based)
       mrname               string         Synonym for rnext
       ncigar               int            Number of cigar operations
       pnext                int            Mate's alignment position (1-based)
       pos                  int            Alignment position (1-based)
       qlen                 int            Alignment length: no. query bases
       qname                string         Query name
       qual                 string         Quality values (raw, 0 based)
       refid                int            Integer reference number (0 based)
       rlen                 int            Alignment length: no. reference bases
       rname                string         Reference name
       rnext                string         Mate's reference name
       sclen                int            Number of soft-clipped bases
       seq                  string         Sequence
       tlen                 int            Template length (insert size)
       [XX]                 int / string   XX tag value

       Flags  are returned either as the whole flag value or by checking for a single bit.  Hence
       the filter expression flag.dup is equivalent to flag & 1024.

       "qlen" and "rlen" are measured using the  CIGAR  string  to  count  the  number  of  query
       (sequence)  and reference bases consumed.  Note "qlen" may not exactly match the length of
       the "seq" field if the sequence is "*".  "sclen" is  the  number  of  soft-clipped  bases.
       When  combined  in  "qlen-sclen"  it  can  give  the  number of sequence bases used in the
       alignment, distinguishing between global alignment and local alignment length.

       "endpos" is the (1-based inclusive) position of the rightmost mapped base of the read,  as
       measured  using  the CIGAR string, and for mapped reads is equivalent to "pos+rlen-1". For
       unmapped reads, it is the same as "pos".

       Reference names may be matched either by their string forms ("rname" and "mrname")  or  as
       the  Nth  @SQ  line  (counting  from  zero)  as  stored  in  BAM  using  "tid"  and "mtid"

       Auxiliary tags are described in square brackets and these  expand  to  either  integer  or
       string  as  defined by the tag itself (XX:Z:string or XX:i:int).  For example [NM]>=10 can
       be used to look for alignments with many mismatches and [RG]=~"grp[ABC]-" will  match  the
       read-group string.

       If  no  comparison  is  used with an auxiliary tag it is taken simply to be a test for the
       existence of that tag.  So [NM] will return any record containing an NM tag, even if  that
       tag  is zero (NM:i:0).  In htslib <= 1.15 negating this with ![NM] gave misleading results
       as it was true if the tag did not exist or did exist but was zero.  Now this  is  strictly
       does-not-exist.   An  explicit exists([NM]) and !exists([NM]) function has also been added
       to make this intention clear.

       Similarly in htslib <= 1.15 using [NM]!=0 was true both when the tag existed and  was  not
       zero  as  well  as when the tag did not exist.  From 1.16 onwards all comparison operators
       are only true for tags that exist, so [NM]!=0 works as expected.

       Some simple functions are available to operate on strings.  These  treat  the  strings  as
       arrays  of  bytes,  permitting  their  length,  minimum,  maximum and average values to be
       computed.  These are useful for processing Quality Scores.

       length(x)   Length of the string (excluding nul char)
       min(x)      Minimum byte value in the string
       max(x)      Maximum byte value in the string
       avg(x)      Average byte value in the string

       Note that "avg" is a floating point value and it may be NAN for empty strings.  This means
       that "avg(qual)" does not produce an error for records that have both seq and qual of "*".
       NAN values will fail any conditional checks, so e.g. "avg(qual) > 20" works and  will  not
       report  these records.  NAN also fails all equality, < and > comparisons, and returns zero
       when given as an argument to the exists function.  It can be negated with !x in which case
       it becomes true.

       Functions that operate on both strings and numerics:

       exists(x)      True if the value exists (or is explicitly true).
       default(x,d)   Value x if it exists or d if not.

       Functions that apply only to numeric values:

       sqrt(x)     Square root of x
       log(x)      Natural logarithm of x
       pow(x, y)   Power function, x to the power of y
       exp(x)      Base-e exponential, equivalent to pow(e,x)


              A  colon-separated  list  of directories in which to search for HTSlib plugins.  If
              $HTS_PATH starts or ends with a colon or contains a double colon (::), the built-in
              list of directories is searched at that point in the search.

              If no HTS_PATH variable is defined, the built-in list of directories specified when
              HTSlib was built is used, which typically  includes  /usr/local/libexec/htslib  and
              similar directories.

              A  colon  separated  (semi-colon on Windows) list of locations in which to look for
              sequences identified by their MD5sums.  This can be either a list of directories or
              URLs.  Note  that if a URL is included then the colon in http:// and ftp:// and the
              optional port number will be treated as part of  the  URL  and  not  a  PATH  field
              separator.  For URLs, the text %s will be replaced by the MD5sum being read.

              If     no     REF_PATH     has     been    specified    it    will    default    to
     and if REF_CACHE is also unset, it will be set
              to  $XDG_CACHE_HOME/hts-ref/%2s/%2s/%s.   If $XDG_CACHE_HOME is unset, $HOME/.cache
              (or a local system temporary directory if no home directory is found) will be  used

              This can be defined to a single location housing a local cache of references.  Upon
              downloading a reference it will be stored in the location pointed to by  REF_CACHE.
              REF_CACHE  will be searched before attempting to load via the REF_PATH search list.
              If no REF_PATH is defined, both REF_PATH and REF_CACHE will  be  automatically  set
              (see  above),  but  if REF_PATH is defined and REF_CACHE not then no local cache is

              To avoid many files being stored in the same directory, REF_CACHE may be defined as
              a pattern using %nums to consume num characters of the MD5sum and %s to consume all
              remaining characters.  If REF_CACHE lacks %s then  it  will  get  an  implicit  /%s

              To aid population of the REF_CACHE directory a script misc/ is
              provided in the Samtools distribution. This takes a fasta file or  a  directory  of
              fasta files and generates the MD5sum named files.

              For  example  if  you  use  seq_cache_populate -subdirs 2 -root /local/ref_cache to
              create 2 nested subdirectories (the default), each consuming 2  characters  of  the
              MD5sum, then REF_CACHE must be set to /local/ref_cache/%2s/%2s/%s.


       o Import SAM to BAM when @SQ lines are present in the header:

           samtools view -b aln.sam > aln.bam

         If @SQ lines are absent:

           samtools faidx ref.fa
           samtools view -bt ref.fa.fai aln.sam > aln.bam

         where ref.fa.fai is generated automatically by the faidx command.

       o Convert a BAM file to a CRAM file using a local reference sequence.

           samtools view -C -T ref.fa aln.bam > aln.cram


       Heng Li from the Sanger Institute wrote the original C version of samtools.  Bob Handsaker
       from the Broad Institute implemented the BGZF library.  Petr Danecek and Heng Li wrote the
       VCF/BCF  implementation.   James  Bonfield  from  the  Sanger Institute developed the CRAM
       implementation.  Other large code contributions have  been  made  by  John  Marshall,  Rob
       Davies,  Martin  Pollard, Andrew Whitwham, Valeriu Ohan (all while primarily at the Sanger
       Institute), with numerous other smaller but valuable contributions.  See  the  per-command
       manual pages for further authorship.


       samtools-addreplacerg(1),  samtools-ampliconclip(1),  samtools-ampliconstats(1), samtools-
       bedcov(1), samtools-calmd(1), samtools-cat(1), samtools-collate(1), samtools-consensus(1),
       samtools-coverage(1),  samtools-depad(1),  samtools-depth(1),  samtools-dict(1), samtools-
       faidx(1), samtools-fasta(1),  samtools-fastq(1),  samtools-fixmate(1),  samtools-flags(1),
       samtools-flagstat(1), samtools-fqidx(1), samtools-head(1), samtools-idxstats(1), samtools-
       import(1), samtools-index(1), samtools-markdup(1), samtools-merge(1), samtools-mpileup(1),
       samtools-phase(1),  samtools-quickcheck(1),  samtools-reference(1),  samtools-reheader(1),
       samtools-rmdup(1),  samtools-sort(1),  samtools-split(1),   samtools-stats(1),   samtools-
       targetcut(1), samtools-tview(1), samtools-view(1), bcftools(1), sam(5), tabix(1)

       Samtools website: <>
       File format specification of SAM/BAM,CRAM,VCF/BCF: <>
       Samtools latest source: <>
       HTSlib latest source: <>
       Bcftools website: <>