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