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sam-stats - Online in the Cloud

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This is the command sam-stats that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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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