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.