JGI_SUMMARIZE_BAM_CONTIG_DEPTHS

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.