Content Comparison

There are two main "eras" of SAMtools development:

• "original" samtools, controlled by author Heng Li
  • v 0.1.19 is the last stable version
• "modern" samtools, controlled by a group of programmers
  • v 1.0, 1.1, 1.2 – avoid these (very buggy!)
  • v 1.3+ – finally stable!

Unfortunately, some functions with the same name in both version eras have different options and arguments! So be sure you know which version you're using. (The samtools version is usually reported at the top of its usage listing).

TACC BioContainers also offers the original samtools version: samtools/ctr-0.1.19--3.

Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]

Options:
  -b       output BAM
  -C       output CRAM (requires -T)
  -1       use fast BAM compression (implies -b)
  -u       uncompressed BAM output (implies -b)
  -h       include header in SAM output
  -H       print SAM header only (no alignments)
  -c       print only the count of matching records
  -o FILE  output file name [stdout]
  -U FILE  output reads not selected by filters to FILE [null]
  -t FILE  FILE listing reference names and lengths (see long help) [null]
  -X       include customized index file
  -L FILE  only include reads overlapping this BED FILE [null]
  -r STR   only include reads in read group STR [null]
  -R FILE  only include reads with read group listed in FILE [null]
  -d STR:STR
           only include reads with tag STR and associated value STR [null]
  -D STR:FILE
           only include reads with tag STR and associated values listed in
           FILE [null]
  -q INT   only include reads with mapping quality >= INT [0]
  -l STR   only include reads in library STR [null]
  -m INT   only include reads with number of CIGAR operations consuming
           query sequence >= INT [0]
  -f INT   only include reads with all  of the FLAGs in INT present [0]
  -F INT   only include reads with none of the FLAGS in INT present [0]
  -G INT   only EXCLUDE reads with all  of the FLAGs in INT present [0]
  -s FLOAT subsample reads (given INT.FRAC option value, 0.FRAC is the
        only include reads withfraction tagof STRtemplates/read andpairs associatedto valuekeep; STRINT [null]part sets seed)
-D STR:FILE -M       use the multi-region iterator only(increases includethe readsspeed, withremoves
tag STR and associated values listed in     duplicates and outputs the reads as they FILEare [null]ordered in the -qfile)
INT  -x onlySTR include reads withread mappingtag qualityto >= INTstrip (repeatable) [0null]
  -lB  STR   only include readscollapse inthe librarybackward STRCIGAR [null]operation
  -m? INT   only include reads withprint numberlong ofhelp, CIGARincluding operationsnote consumingabout region specification
  -S       queryignored sequence(input >=format INT [0]is auto-detected)
  --no-fPG INT do not onlyadd includea readsPG withline
all  of the FLAGs in INT present [0 --input-fmt-option OPT[=VAL]
  -F INT   only include reads with none of the FLAGS in INTSpecify presenta [0]single input file -Gformat INToption in the onlyform
EXCLUDE reads with all  of the FLAGs in INT present [0]   -s FLOATof subsampleOPTION reads (given INT.FRAC option value, 0.FRAC is theor OPTION=VALUE
  -O, --output-fmt FORMAT[,OPT[=VAL]]...
             fraction of templates/readSpecify pairsoutput to keep; INT part sets seed)format (SAM, BAM, CRAM)
   -M   --output-fmt-option OPT[=VAL]
  use the multi-region iterator (increases the speed, removes      Specify a single output file format duplicatesoption and outputsin the readsform
as they are ordered in the file)   -x STR   read tag toof stripOPTION (repeatable) [null]or OPTION=VALUE
  -BT, --reference FILE
    collapse the backward CIGAR operation   -?    Reference sequence FASTA printFILE long[null]
help, including note about region specification-@, --threads INT
   -S       ignored (input format is auto-detected) Number of --no-PGadditional threads doto not add a PG lineuse [0]
      --inputwrite-fmt-option OPT[=VAL]index
               Automatically Specifyindex athe singleoutput inputfiles file[off]
format option in the form  --verbosity INT
            of OPTION or OPTION=VALUESet level  -O, --output-fmt FORMAT[,OPT[=VAL]]...
               Specify output format (SAM, BAM, CRAM)
      --output-fmt-option OPT[=VAL]
               Specify a single output file format option in the form
               of OPTION or OPTION=VALUE
  -T, --reference FILE
               Reference sequence FASTA FILE [null]
  -@, --threads INT
               Number of additional threads to use [0]
      --write-index
               Automatically index the output files [off]
      --verbosity INT
               Set level of verbosity

cd $SCRATCH/core_ngs/alignment/yeast_bwa
samtools view -b yeast_pe.sam > yeast_pe.bam 

samtools view yeast_pe.bam | more

Note that samtools (like bwa) writes its help to standard error, but less and more only accept input on standard input. So the syntax redirecting standard error to standard input must be used before the pipe to less or more.

samtools view 2>&1 | less -I

then search for "header" ( /header )

samtools view -h shows both header and alignment records.

samtools view -H shows header records only.

samtools view yeast_pe.bam | cut -f 1-4 | more

Usage: samtools sort [options...] [in.bam]
Options:
  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)
  -u         Output uncompressed data (equivalent to -l 0)
  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]
  -M         Use minimiser for clustering unaligned/unplaced reads
  -R         Do not use reverse strand (only compatible with -M)
  -K INT     Kmer size to use for minimiser [20]
  -I FILE    Order minimisers by their position in FILE FASTA
  -w INT     Window size for minimiser indexing via -I ref.fa [100]
  -H         Squash homopolymers when computing minimiser
  -n         Sort by read name (natural): cannot be used with samtools index
  -N         Sort by read name (ASCII): cannot be used with samtools index
  -t TAG     Sort by value of TAG. Uses position as secondary index (or read name if -n is set)
  -o FILE    Write final output to FILE rather than standard output
  -T PREFIX  Write temporary files to PREFIX.nnnn.bam
      --no-PG
               Do not add a PG line
      --template-coordinate
          -T PREFIX  Write temporary filesSort to PREFIX.nnnn.bamby template-coordinate
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
              
of OPTION or OPTION=VALUE
  -O, --output-fmt FORMAT[,OPT[=VAL]]...
               Specify output format (SAM, BAM, CRAM)
      --output-fmt-option OPT[=VAL]
               Specify a single output file format option in the form
             
 of OPTION or OPTION=VALUE
      --reference FILE
               Reference sequence FASTA FILE [null]
  -@, --threads INT
               Number of additional threads to use [0]
      --write-index
               Automatically index the output files [off]
      --verbosity INT
               Set level of verbosity