.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH JGI_SUMMARIZE_BAM_CONTIG_DEPTHS "1" "May 2020" "jgi_summarize_bam_contig_depths 2.15" "User Commands"
.SH NAME
jgi_summarize_bam_contig_depths \- jgi_summarize_bam_contig_depths nosha
.SH SYNOPSIS
.B jgi_summarize_bam_contig_depths
\fI\,<options> sortedBam1 \/\fR[ \fI\,sortedBam2 \/\fR...]
.SH OPTIONS
.TP
\fB\-\-outputDepth\fR
arg  The file to put the contig by bam depth matrix (default: STDOUT)
.TP
\fB\-\-percentIdentity\fR
arg  The minimum end\-to\-end % identity of qualifying reads (default: 97)
.TP
\fB\-\-pairedContigs\fR
arg  The file to output the sparse matrix of contigs which paired reads span (default: none)
.TP
\fB\-\-unmappedFastq\fR
arg  The prefix to output unmapped reads from each bam file suffixed by 'bamfile.bam.fastq.gz'
.TP
\fB\-\-noIntraDepthVariance\fR
Do not include variance from mean depth along the contig
.TP
\fB\-\-showDepth\fR
Output a .depth file per bam for each contig base
.TP
\fB\-\-minMapQual\fR
arg  The minimum mapping quality necessary to count the read as mapped (default: 0)
.TP
\fB\-\-weightMapQual\fR
arg  Weight per\-base depth based on the MQ of the read (i.e uniqueness) (default: 0.0 (disabled))
.TP
\fB\-\-includeEdgeBases\fR
When calculating depth & variance, include the 1\-readlength edges (off by default)
.TP
\fB\-\-maxEdgeBases\fR
When calculating depth & variance, and not \fB\-\-includeEdgeBases\fR, the maximum length (default:75)
.TP
\fB\-\-referenceFasta\fR
arg  The reference file.  (It must be the same fasta that bams used)
.PP
Options that require a \fB\-\-referenceFasta\fR
.TP
\fB\-\-outputGC\fR
arg  The file to print the gc coverage histogram
.TP
\fB\-\-gcWindow\fR
arg  The sliding window size for GC calculations
.TP
\fB\-\-outputReadStats\fR
arg  The file to print the per read statistics
.TP
\fB\-\-outputKmers\fR
arg  The file to print the perfect kmer counts
.PP
Options to control shredding contigs that are under represented by the reads
.TP
\fB\-\-shredLength\fR
arg  The maximum length of the shreds
.TP
\fB\-\-shredDepth\fR
arg  The depth to generate overlapping shreds
.TP
\fB\-\-minContigLength\fR
arg  The mimimum length of contig to include for mapping and shredding
.TP
\fB\-\-minContigDepth\fR
arg  The minimum depth along contig at which to break the contig
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.