Emits a data file containing information about callable, uncallable, poorly mapped, and other parts of the genome
A very common question about a NGS set of reads is what areas of the genome are considered callable. The system considers the coverage at each locus and emits either a per base state or a summary interval BED file that partitions the genomic intervals into the following callable states:
A BAM file containing exactly one sample.
java -jar GenomeAnalysisTK.jar \ -T CallableLoci \ -I my.bam \ -summary my.summary \ -o my.bedwould produce a BED file (my.bed) that looks like:
20 10000000 10000864 PASS 20 10000865 10000985 POOR_MAPPING_QUALITY 20 10000986 10001138 PASS 20 10001139 10001254 POOR_MAPPING_QUALITY 20 10001255 10012255 PASS 20 10012256 10012259 POOR_MAPPING_QUALITY 20 10012260 10012263 PASS 20 10012264 10012328 POOR_MAPPING_QUALITY 20 10012329 10012550 PASS 20 10012551 10012551 LOW_COVERAGE 20 10012552 10012554 PASS 20 10012555 10012557 LOW_COVERAGE 20 10012558 10012558 PASS et cetera...as well as a summary table that looks like:
state nBases REF_N 0 PASS 996046 NO_COVERAGE 121 LOW_COVERAGE 928 EXCESSIVE_COVERAGE 0 POOR_MAPPING_QUALITY 2906
These Read Filters are automatically applied to the data by the Engine before processing by CallableLoci.
This tool overrides the engine's default downsampling settings.
The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
|--summary||File||NA||Name of file for output summary|
|--out||PrintStream||stdout||An output file created by the walker. Will overwrite contents if file exists|
|-frlmq||double||0.1||If the fraction of reads at a base with low mapping quality exceeds this value, the site may be poorly mapped|
|--maxDepth||int||-1||Maximum read depth before a locus is considered poorly mapped|
|--maxLowMAPQ||byte||1||Maximum value for MAPQ to be considered a problematic mapped read.|
|--minBaseQuality||byte||20||Minimum quality of bases to count towards depth.|
|--minMappingQuality||byte||10||Minimum mapping quality of reads to count towards depth.|
|--minDepth||int||4||Minimum QC+ read depth before a locus is considered callable|
|--minDepthForLowMAPQ||int||10||Minimum read depth before a locus is considered a potential candidate for poorly mapped|
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
Output format. The output of this walker will be written in this format. The recommended option is BED.
The --format argument is an enumerated type (OutputFormat), which can have one of the following values:
If the fraction of reads at a base with low mapping quality exceeds this value, the site may be poorly mapped. If the number of reads at this site is greater than minDepthForLowMAPQ and the fraction of reads with low mapping quality exceeds this fraction then the site has POOR_MAPPING_QUALITY.
Maximum read depth before a locus is considered poorly mapped. If the QC+ depth exceeds this value the site is considered to have EXCESSIVE_DEPTH
Maximum value for MAPQ to be considered a problematic mapped read.. The gap between this value and mmq are reads that are not sufficiently well mapped for calling but aren't indicative of mapping problems. For example, if maxLowMAPQ = 1 and mmq = 20, then reads with MAPQ == 0 are poorly mapped, MAPQ >= 20 are considered as contributing to calling, where reads with MAPQ >= 1 and < 20 are not bad in and of themselves but aren't sufficiently good to contribute to calling. In effect this reads are invisible, driving the base to the NO_ or LOW_COVERAGE states
Minimum quality of bases to count towards depth.. Bases with less than minBaseQuality are viewed as not sufficiently high quality to contribute to the PASS state
Minimum QC+ read depth before a locus is considered callable. If the number of QC+ bases (on reads with MAPQ > minMappingQuality and with base quality > minBaseQuality) exceeds this value and is less than maxDepth the site is considered PASS.
Minimum read depth before a locus is considered a potential candidate for poorly mapped. We don't want to consider a site as POOR_MAPPING_QUALITY just because it has two reads, and one is MAPQ. We won't assign a site to the POOR_MAPPING_QUALITY state unless there are at least minDepthForLowMAPQ reads covering the site.
Minimum mapping quality of reads to count towards depth.. Reads with MAPQ > minMappingQuality are treated as usable for variation detection, contributing to the PASS state.
An output file created by the walker. Will overwrite contents if file exists.
Name of file for output summary. Callable loci summary counts (see outputs) will be written to this file.
GATK version 2.7-4-g46ca8c7 built at 2013/10/10 17:33:37.