.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
.TH SAM-STATS "1" "July 2015" "sam-stats 1.1.2" "User Commands"
.SH NAME
sam-stats \- ea-utils: produce digested statistics
.SH SYNOPSIS
.B sam-stats
[\fI\,options\/\fR] [\fI\,file1\/\fR] [\fI\,file2\/\fR...\fI\,filen\/\fR]
.SH DESCRIPTION
Version: 1.38.681
.PP
Produces lots of easily digested statistics for the files listed
.PP
Options (default in parens):
.PP
\fB\-D\fR             Keep track of multiple alignments
\fB\-O\fR PREFIX      Output prefix enabling extended output (see below)
\fB\-R\fR FIL         Coverage/RNA output (coverage, 3' bias, etc, implies \fB\-A\fR)
\fB\-A\fR             Report all chr sigs, even if there are more than 1000
\fB\-b\fR INT         Number of reads to sample for per\-base stats (1M)
\fB\-S\fR INT         Size of ascii\-signature (30)
\fB\-x\fR FIL         File extension for handling multiple files (stats)
\fB\-M\fR             Only overwrite if newer (requires \fB\-x\fR, or multiple files)
\fB\-B\fR             Input is bam, don't bother looking at magic
\fB\-z\fR             Don't fail when zero entries in sam
.PP
OUTPUT:
.PP
If one file is specified, then the output is to standard out.  If
multiple files are specified, or if the \fB\-x\fR option is supplied,
the output file is <filename>.<ext>.  Default extension is 'stats'.
.PP
Complete Stats:
.TP
<STATS>
: mean, max, stdev, median, Q1 (25 percentile), Q3
.TP
reads
: # of entries in the sam file, might not be # reads
.TP
phred
: phred scale used
.TP
bsize
: # reads used for qual stats
.TP
mapped reads
: number of aligned reads (unique probe id sequences)
.TP
mapped bases
: total of the lengths of the aligned reads
.TP
forward
: number of forward\-aligned reads
.TP
reverse
: number of reverse\-aligned reads
.TP
snp rate
: mismatched bases / total bases (snv rate)
.TP
ins rate
: insert bases / total bases
.TP
del rate
: deleted bases / total bases
.TP
pct mismatch
: percent of reads that have mismatches
.TP
pct align
: percent of reads that aligned
.TP
len <STATS>
: read length stats, ignored if fixed\-length
.TP
mapq <STATS>
: stats for mapping qualities
.TP
insert <STATS>
: stats for insert sizes
.TP
%<CHR>
: percentage of mapped bases per chr, followed by a signature
.SS "Subsampled stats (1M reads max):"
.IP
base qual <STATS> : stats for base qualities
%A,%T,%C,%G       : base percentages
.SS "Meaning of the per-chromosome signature:"
.IP
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'.
.SS "Extended output mode produces a set of files:"
.TP
\&.stats
: primary output
.TP
\&.fastx
: fastx\-toolkit compatible output
.TP
\&.rcov
: per\-reference counts & coverage
.TP
\&.xdist
: mismatch distribution
.TP
\&.ldist
: length distribution (if applicable)
.TP
\&.mqdist
: mapping quality distribution