---
name: "jgi_summarize_bam_contig_depths"
section: "1"
platform: "linux"
package: "metabat"
version: "2.15-4+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/jgi_summarize_bam_contig_depths"
---

# jgi\_summarize\_bam\_contig\_depths(1)

jgi\_summarize\_bam\_contig\_depths nosha

## NAME

jgi\_summarize\_bam\_contig\_depths - jgi\_summarize\_bam\_contig\_depths nosha

## SYNOPSIS

**jgi\_summarize\_bam\_contig\_depths** *\<options\> sortedBam1* \[ *sortedBam2* ...\]

## OPTIONS

- **--outputDepth**

  arg  The file to put the contig by bam depth matrix (default: STDOUT)

- **--percentIdentity**

  arg  The minimum end-to-end % identity of qualifying reads (default: 97)

- **--pairedContigs**

  arg  The file to output the sparse matrix of contigs which paired reads span (default: none)

- **--unmappedFastq**

  arg  The prefix to output unmapped reads from each bam file suffixed by 'bamfile.bam.fastq.gz'

- **--noIntraDepthVariance**

  Do not include variance from mean depth along the contig

- **--showDepth**

  Output a .depth file per bam for each contig base

- **--minMapQual**

  arg  The minimum mapping quality necessary to count the read as mapped (default: 0)

- **--weightMapQual**

  arg  Weight per-base depth based on the MQ of the read (i.e uniqueness) (default: 0.0 (disabled))

- **--includeEdgeBases**

  When calculating depth & variance, include the 1-readlength edges (off by default)

- **--maxEdgeBases**

  When calculating depth & variance, and not **--includeEdgeBases**, the maximum length (default:75)

- **--referenceFasta**

  arg  The reference file.  (It must be the same fasta that bams used)

Options that require a **--referenceFasta**

- **--outputGC**

  arg  The file to print the gc coverage histogram

- **--gcWindow**

  arg  The sliding window size for GC calculations

- **--outputReadStats**

  arg  The file to print the per read statistics

- **--outputKmers**

  arg  The file to print the perfect kmer counts

Options to control shredding contigs that are under represented by the reads

- **--shredLength**

  arg  The maximum length of the shreds

- **--shredDepth**

  arg  The depth to generate overlapping shreds

- **--minContigLength**

  arg  The mimimum length of contig to include for mapping and shredding

- **--minContigDepth**

  arg  The minimum depth along contig at which to break the contig

## AUTHOR

 This manpage was written by Andreas Tille for the Debian distribution and\
  can be used for any other usage of the program.