Content Comparison

idev -m 180120 -N 1 -A OTH21164 -r core-ngs-class-0605

The bwa aln usage doesn't say anything about the program's diagnostic output, so we can assume it will be written to standard error. So it could be redirected like this:

bwa aln -t 60 sacCer3/sacCer3.fa \
  fastq/Sample_Yeast_L005_R2.cat.fastq.gz \
  > yeast_pe_R2.sai 2> yeast_pe_R2.log

wc -l yeast_pe.sam  reports 1,184,378 lines

The alignment SAM file will contain records for both R1 and R2 reads, so we need to count sequences in both files.

zcat ./fastq/Sample_Yeast_L005_R[12]*gz | wc -l | awk '{print $1/4}' reports 1,184,360 reads that were alignedread sequences.

So the SAM file has 18 more lines than the R1+R2 total. These are the header records that appear before any alignment records.

Program: samtools (Tools for alignments in the SAM format)
Version: 1.920 (using htslib 1.920)

Usage:   samtools <command> [options]

Commands:
 
-- Indexing
 
   dict           create a sequence dictionary file

    faidx          index/extract FASTA
     fqidx          index/extract FASTQ

    index          index alignment

  -- Editing
     calmd          recalculate MD/NM tags and '=' bases
 
   fixmate        fix mate information
 
   reheader       replace BAM header
 
   targetcut      cut fosmid regions (for fosmid pool only)
 
   addreplacerg   adds or replaces RG tags
 
   markdup        mark duplicates
   ampliconclip   clip oligos from the end of reads

-- File operations
 
   collate        shuffle and group alignments by name
 
   cat            concatenate BAMs
   consensus      produce a consensus Pileup/FASTA/FASTQ
   merge          merge sorted alignments
     mpileup        multi-way pileup
 
   sort           sort alignment file
     split          splits a file by read group
     quickcheck     quickly check if SAM/BAM/CRAM file appears intact
     fastq          converts a BAM to a FASTQ
 
   fasta          converts a BAM to a FASTA
   --import Statistics      bedcov  Converts FASTA or FASTQ files to SAM/BAM/CRAM
read depth per BEDreference region     Generates coveragea reference from aligned data
  alignment depthreset and percent coverage      depth Reverts aligner changes in reads

-- Statistics
 compute the depthbedcov      flagstat   read depth per BED simpleregion
stats   coverage   idxstats    alignment depth and BAMpercent indexcoverage
stats   depth   phase       compute the depth
phase heterozygotes  flagstat    stats   simple stats
   idxstats  generate stats (former bamcheck)  BAM index --stats
Viewing   cram-size   flags   list CRAM Content-ID and Data-Series sizes
 explain BAM flagsphase      tview    phase heterozygotes
   stats text alignment viewer      view generate stats (former bamcheck)
   ampliconstats  generate amplicon specific stats

-- Viewing
   flags explain  BAM flags
   head           header viewer
   tview text     alignment viewer
   view           SAM<->BAM<->CRAM conversion
 
   depad          convert padded BAM to unpadded BAM

   samples        list the samples in a set of SAM/BAM/CRAM files

-- Misc
   help [cmd]     display this help message or help for [cmd]
   version        detailed version information

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 )

Usage: samtools sort [options...] [in.bam]
Options:
  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)
  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]
  -n         Sort by read name: 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
               Sort by 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      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