Depth of Coverage
From GSA
See Depth of Coverage v3.0 for the current tool
Warning: the material on this page is considered out of date by the GSA team.
Contents |
Depth of coverage
Displays the depth of coverage at all covered loci.
Input
Reads and reference.
Optionally allows the following arguments:
- --printStyle, -s
- One of NONE, COMPACT (the default), or DETAILED. If NONE, no per-locus output is produced, only the traversal results will be displayed. If COMPACT, only the total coverage at each locus will be printed. IF DETAILED, then total, clean reads, reads with deletions, and reads with MAPQ below the threshold will be displayed separately.
- --excludeDeletions, -ed
- If true, we will exclude reads with deletions at a locus in coverage
- --minMAPQ, -minMAPQ
- If provided, we will exclude reads with MAPQ < this value at a locus in coverage
Output
If locus printing is enabled, displays one locus per line along with the number of reads overlapping that locus. Always prints out a summary indicating average depth of coverage for each specified interval, or the entire genome if no interval was specified.
Example
java -jar /home/radon01/depristo/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar \ -L 1:10,164,500-10,164,520\;1:10,164,550-10,164,560 \ -R /broad/1KG/reference/human_b36_both.fasta \ -T DepthOfCoverage \ -I /broad/hptmp/ebanks/1kg_pilot2/CLEANED_SOLEXA_BAMS/NA12878.chr1.full.bam \ -s DETAILED
Sample output:
INFO 08:43:40,062 CommandLineProgram - ------------------------------------------------------- INFO 08:43:40,077 CommandLineProgram - The Genome Analysis Toolkit (GATK) INFO 08:43:40,078 CommandLineProgram - Copyright (c) 2009 The Broad Institute INFO 08:43:40,078 CommandLineProgram - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 08:43:40,079 CommandLineProgram - For support, email gsadevelopers@broadinstitute.org INFO 08:43:40,079 CommandLineProgram - INFO 08:43:40,080 CommandLineProgram - Program Args: -L 1:10,164,500-10,164,520;1:10,164,550-10,164,560 -R /broad/1KG/reference/human_b36_both.fasta -T DepthOfCoverage -I /broad/hptmp/ebanks/1kg_pilot2/CLEANED_SOLEXA_BAMS/NA12878.chr1.full.bam -s DETAILED INFO 08:43:40,080 CommandLineProgram - Time/Date: 2009/09/09 08:43:40 INFO 08:43:40,081 CommandLineProgram - ------------------------------------------------------- /broad/hptmp/ebanks/1kg_pilot2/CLEANED_SOLEXA_BAMS/NA12878.chr1.full.bam locus nCleanRead nDeltionReads nLowMAPQReads 1:10164500 8 8 0 0 1:10164501 8 8 0 0 1:10164502 7 7 0 0 1:10164503 6 6 0 0 1:10164504 8 8 0 0 1:10164505 8 8 0 0 1:10164506 8 8 0 0 1:10164507 9 9 0 0 1:10164508 10 10 0 0 1:10164509 10 6 4 0 1:10164510 10 6 4 0 1:10164511 9 9 0 0 1:10164512 9 9 0 0 1:10164513 9 9 0 0 1:10164514 9 9 0 0 1:10164515 9 9 0 0 1:10164516 9 9 0 0 1:10164517 10 10 0 0 1:10164518 10 10 0 0 1:10164519 9 9 0 0 1:10164520 9 9 0 0 1:10164550 21 21 0 0 1:10164551 23 23 0 0 1:10164552 23 23 0 0 1:10164553 22 22 0 0 1:10164554 22 22 0 0 1:10164555 22 22 0 0 1:10164556 24 24 0 0 1:10164557 23 23 0 0 1:10164558 24 24 0 0 1:10164559 23 23 0 0 1:10164560 25 25 0 0 [INTERVAL REDUCE RESULT] at 1:10164500-10164520 Average depth of coverage is: 8.76 in 184 total coverage over 21 sites [INTERVAL REDUCE RESULT] at 1:10164550-10164560 Average depth of coverage is: 22.91 in 252 total coverage over 11 sites
