Depth_histo

Format

cg depth_histo ?options? bamfile ?regionfile?

Summary

makes a histogram of the depth in the given bamfile, subdivided in on- and oftarget regions

Description

depth_histo outputs a tsv formatted histogram of the depth: For each depth (column depth) the number of bases with this depth are given in the target region (column ontarget) and outside the target region (column offtarget). The target region is given in the regionfile in tsv format. The histogram is by default limited to a maximum depth of 1000 (Positions with a depth >= 1000 are counted as depth 1000). This can be changed with the -max option. Depths not presents in are skipped in the output

Options

-max maxnum: The maximum depth in the histogram (default = 1000). Positions with a depth >= maxnum are counted as depth maxnum
-q num: Only count reads with base quality greater than num
-Q num: Only count reads with mapping quality greater than num

Arguments

bamfile: bamfile
regionfile: target regions. If no target regionfile is given, all bases will be counted in offtarget

Example

cg depth_histo test.bam regfile.tsv > histo.tsv

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