NAME

       sam-stats - ea-utils: produce digested statistics

SYNOPSIS

       sam-stats [options] [file1] [file2...filen]

DESCRIPTION

       Version: 1.38.681

       Produces lots of easily digested statistics for the files listed

       Options (default in parens):

       -D              Keep  track  of multiple alignments -O PREFIX      Output prefix enabling extended output
       (see below) -R FIL         Coverage/RNA output (coverage, 3' bias, etc, implies -A) -A             Report
       all chr sigs, even if there are more than 1000 -b INT         Number of  reads  to  sample  for  per-base
       stats  (1M)  -S  INT          Size  of  ascii-signature  (30)  -x FIL         File extension for handling
       multiple files (stats) -M             Only overwrite  if  newer  (requires  -x,  or  multiple  files)  -B
       Input is bam, don't bother looking at magic -z             Don't fail when zero entries in sam

       OUTPUT:

       If one file is specified, then the output is to standard out.  If multiple files are specified, or if the
       -x option is supplied, the output file is <filename>.<ext>.  Default extension is 'stats'.

       Complete Stats:

       <STATS>
              : mean, max, stdev, median, Q1 (25 percentile), Q3

       reads  : # of entries in the sam file, might not be # reads

       phred  : phred scale used

       bsize  : # reads used for qual stats

       mapped reads
              : number of aligned reads (unique probe id sequences)

       mapped bases
              : total of the lengths of the aligned reads

       forward
              : number of forward-aligned reads

       reverse
              : number of reverse-aligned reads

       snp rate
              : mismatched bases / total bases (snv rate)

       ins rate
              : insert bases / total bases

       del rate
              : deleted bases / total bases

       pct mismatch
              : percent of reads that have mismatches

       pct align
              : percent of reads that aligned

       len <STATS>
              : read length stats, ignored if fixed-length

       mapq <STATS>
              : stats for mapping qualities

       insert <STATS>
              : stats for insert sizes

       %<CHR> : percentage of mapped bases per chr, followed by a signature

   Subsampled stats (1M reads max):
              base qual <STATS> : stats for base qualities %A,%T,%C,%G       : base percentages

   Meaning of the per-chromosome signature:
              A  ascii-histogram  of  mapped  reads  by  chromosome position.  It is only output if the original
              SAM/BAM has a header. The values are the log2 of the # of mapped reads at each  position  +  ascii
              '0'.

   Extended output mode produces a set of files:
       .stats : primary output

       .fastx : fastx-toolkit compatible output

       .rcov  : per-reference counts & coverage

       .xdist : mismatch distribution

       .ldist : length distribution (if applicable)

       .mqdist
              : mapping quality distribution

sam-stats 1.1.2                                     July 2015                                       SAM-STATS(1)