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Samtools depth (version 1.15.1+galaxy2)

BAM file(s):

Filter by regions:

Output all positions:

Note that if the all option (-a) is used in conjunction with a BED file it may sometimes operate as if -aa was specified if the reference sequence has coverage outside of the region specified in the BED file.

Ignore reads shorter than:

Limits the maximum number of considered alignments starting at any sequence position to INT. Note that, the reported depths values might be larger than INT. If 0, depth is set to the maximum integer value, effectively removing any depth limit. (default = 8000):

Only count reads with base quality greater than:

Only count reads with mapping quality greater than:

Additional Filter Options

Additional Filter Options 0

Output Options

Output Options 0

What it does

Computes the depth at each position or region using the samtools depth command.

The output is a tabular file, with one line for each base of each reference with any coverage (bases with no coverage may not appear).

The first column is the reference name, the second column is the reference position, and then there is one column for each SAM/BAM file giving the coverage depth at that position.