jgi_summarize_bam_contig_depths - jgi_summarize_bam_contig_depths nosha

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

jgi_summarize_bam_contig_depths 2.15                May 2020                  JGI_SUMMARIZE_BAM_CONTIG_DEPTHS(1)

       jgi_summarize_bam_contig_depths - jgi_summarize_bam_contig_depths nosha

--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

jgi_summarize_bam_contig_depths<options>sortedBam1 [ sortedBam2 ...]