# CallableLoci

Emits a data file containing information about callable, uncallable, poorly mapped, and other parts of the genome

## Overview

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:

REF_N
the reference base was an N, which is not considered callable the GATK
PASS
the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE
NO_COVERAGE
absolutely no reads were seen at this locus, regardless of the filtering parameters
LOW_COVERAGE
there were less than min. depth bases at the locus, after applying filters
EXCESSIVE_COVERAGE
more than -maxDepth read at the locus, indicating some sort of mapping problem
POOR_MAPPING_QUALITY
more than --maxFractionOfReadsWithLowMAPQ at the locus, indicating a poor mapping quality of the reads

### Input

A BAM file containing exactly one sample.

### Output

• -o: a OutputFormatted (recommended BED) file with the callable status covering each base
• -summary: a table of callable status x count of all examined bases

### Examples

  java -jar GenomeAnalysisTK.jar \
-T CallableLoci \
-I my.bam \
-summary my.summary \
-o my.bed


would 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.

### Downsampling settings

This tool applies the following downsampling settings by default.

• Mode: BY_SAMPLE
• To coverage: 1,000

## Command-line Arguments

### Inherited arguments

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).

### CallableLoci specific arguments

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
NA 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
-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.
--format
NA 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

### Argument details

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.

### --format / -format

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:

BED
The output will be written as a BED file. There's a BED element for each continuous run of callable states (i.e., PASS, REF_N, etc). This is the recommended format
STATE_PER_BASE
Emit chr start stop state quads for each base. Produces a potentially disasterously large amount of output.

OutputFormat

### --maxDepth / -maxDepth

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  [ [ -∞  ∞ ] ]

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  [ [ -∞  ∞ ] ]

### --maxLowMAPQ / -mlmq

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  [ [ -∞  ∞ ] ]

### --minBaseQuality / -mbq

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  [ [ -∞  ∞ ] ]

### --minDepth / -minDepth

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  [ [ -∞  ∞ ] ]

### --minDepthForLowMAPQ / -mdflmq

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  [ [ -∞  ∞ ] ]

### --minMappingQuality / -mmq

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  [ [ -∞  ∞ ] ]

### --out / -o

An output file created by the walker. Will overwrite contents if file exists

PrintStream

### --summary / -summary

Name of file for output summary
Callable loci summary counts (see outputs) will be written to this file.

R File