Introduction

Tool for computing statistics from (possibly compressed) SAM or BAM files.

Details

sam-stats [options] <sam or bam file>

Options:
  -h                : this help
  -b                : base sample size (5000)
  -c                : read sample count (0)

OUTPUT:

Complete Stats:

  <STATS>           : mean, max, stdev, median, Q1 (25 percentile), Q3
  reads             : # of entries in the file
  phred             : phred scale used
  mapped reads      : number of aligned reads
  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
  ins rate          : inserted bases / total bases
  del rate          : deleted bases / total bases
  pct mismatch      : percent of reads that have mismatches
  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 chromosome (use to compute coverage)

Subsampled stats:
  base qual <STATS> : stats for base qualities
  %A,%T,%C,%G       : base percentages

Example (Single-end RNA w/bowtie, hence the odd distribution & no indels or mate info):

reads   110836000
phred   33
mapped reads    110836000
mapped bases    8756752622
foward  54636749
reverse 56199251
len max 80.0000
len mean        79.0064
len stdev       5.4687
mapq mean       170.5078
mapq stdev      119.6054
mapq Q1 3.0000
mapq median     255.0000
mapq Q3 255.0000
snp rate        0.003512
pct mismatch    21.4714
base qual mean  36.9820
base qual stdev 4.6959
%A      25.8659
%C      22.7026
%G      25.8926
%T      25.4710
%N      0.0679
%chr1   6.42
%chr10  2.41
%chr11  3.58
%chr12  7.57
%chr13  1.93
%chr14  2.12
%chr15  2.48
%chr16  1.81
%chr17  2.68
%chr18  1.92
%chr19  2.78
%chr2   3.75
%chr3   3.99
%chr4   26.81
%chr5   8.29
%chr6   3.70
%chr7   3.85
%chr8   2.67
%chr9   3.77
%chrM   6.25
%chrX   1.21
%chrY   0.01