jgi_summarize_bam_contig_depths1

Usage

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