sam-stats1
Ea-utils: produce digested statistics
Usage
sam-stats [options]
[file1]
[file2 ...
filen]
Overview
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 |
Releases
Unchanged in 5 releases since Debian 9 (Stretch).