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Samtools stats (version 2.0.9)

BAM file:

Set coverage distribution:

Exclude reads marked as duplicates:

Output:

Select between one single output or separate outputs for each statistics

Filter by SAM flags:

More info on the flags: https://samtools.github.io/hts-specs/SAMv1.pdf

Size of GC-depth bins:

Decreasing bin size increases memory requirement. default=2e4

Maximum insert size:

default=8000

Limit to a specific read group name:

Minimum read length to generate statistics for:

No cutoff if left empty

Report only the main part of inserts:

default=0.99

BWA trim parameter:

default=0

Use a reference sequence:

Required for GC-depth and mismatches-per-cycle calculation

Filter by regions:

restricts output to only those alignments which overlap the specified region(s)

Suppress absence of insertions:

Suppress outputting IS rows where there are no insertions.

Remove overlaps of paired-end reads from coverage and base count computations:

Only bases with coverage above this value will be included in the target percentage computation:

What it does

This tool runs the samtools stats command.

The results of samtools stats can be visualized with MultiQC (for this the default of a single output file needs to be selected).