Collect statistics on 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. This tool 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.
A file with the callable status covering each base and a table of callable status x count of all examined bases
java -jar GenomeAnalysisTK.jar \
-T CallableLoci \
-R reference.fasta \
-I myreads.bam \
-summary table.txt \
-o callable_status.bed
would produce a BED file 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
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 applies the following downsampling settings by default.
All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Outputs | |||
| --summary |
NA | Name of file for output summary | |
| Optional Outputs | |||
| --out -o |
stdout | An output file created by the walker. Will overwrite contents if file exists | |
| Optional Parameters | |||
| --maxDepth |
-1 | Maximum read depth before a locus is considered poorly mapped | |
| --maxFractionOfReadsWithLowMAPQ -frlmq |
0.1 | If the fraction of reads at a base with low mapping quality exceeds this value, the site may be poorly mapped | |
| --maxLowMAPQ -mlmq |
1 | Maximum value for MAPQ to be considered a problematic mapped read. | |
| --minBaseQuality -mbq |
20 | Minimum quality of bases to count towards depth. | |
| --minMappingQuality -mmq |
10 | Minimum mapping quality of reads to count towards depth. | |
| Advanced Parameters | |||
| --format |
BED | Output format | |
| --minDepth |
4 | Minimum QC+ read depth before a locus is considered callable | |
| --minDepthForLowMAPQ -mdflmq |
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 tool 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:
OutputFormat BED
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
int -1 [ [ -∞ ∞ ] ]
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.
double 0.1 [ [ -∞ ∞ ] ]
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
byte 1 [ [ -∞ ∞ ] ]
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
byte 20 [ [ -∞ ∞ ] ]
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.
int 4 [ [ -∞ ∞ ] ]
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.
int 10 [ [ -∞ ∞ ] ]
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.
byte 10 [ [ -∞ ∞ ] ]
An output file created by the walker. Will overwrite contents if file exists
PrintStream stdout
Name of file for output summary
Callable loci summary counts will be written to this file.
R File NA