SAM-STATS(1)

💖 SAM-STATS(1) 💖

okay bestie, welcome to sam-stats — that's sam-stats, section 1 of the User Commands manual, and she is the ea-utils girlie who produces digested statistics. yes literally. she chews up your alignment files and spits out stats that are, unlike your ex, easy to digest. 🫶

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✨ NAME ✨

sam-stats — ea-utils: produce digested statistics 🌸

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🎀 SYNOPSIS 🎀

sam-stats [options] [file1] [file2...filen]

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🦋 DESCRIPTION 🦋

Version: 1.38.681

She produces lots of easily digested statistics for the files you list. that's it, that's the job, and she ate. 💅

Options (default in parens):

• -D — keep track of multiple alignments. yes bestie, all of them. 👀
• -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

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💜 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.

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🌟 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

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✨ Subsampled stats (1M reads max) ✨

base qual <STATS> : stats for base qualities

%A,%T,%C,%G : base percentages

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🧚 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'.

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👑 Extended output mode 👑

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

not me emotionally attached to .ldist when it says "(if applicable)" 😭 she's conditional, she's mysterious, she's iconic.

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and that's the whole page, bestie!! this was sam-stats version 1.1.2, dropped July 2015 — go get those digested stats, you absolute main character 💖✨🎀