sam-stats - Online in the Cloud

PROGRAM:

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

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