Showing docs for version 3.7-0

CompareCallableLoci

Compare callability statistics

Category Diagnostics and Quality Control Tools

Traversal LocusWalker

PartitionBy LOCUS

Overview

This tool can be used to evaluate how different sequence datasets compare in terms of "callability" based on the output of the CallableLoci tool.

Input

Two files to compare, output by two runs of CallableLoci

Output

A table showing the callability status of each interval of interest in the two comparison sets and whether they match.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -R reference.fasta \
   -T CompareCallableLoci \
   -comp1 callable_loci_1.bed \
   -comp2 callable_loci_2.bed \
   [-L input.intervals \]
   -o comparison.table

Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by CompareCallableLoci.

Command-line Arguments

Engine arguments

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.

CommandLineGATK

CompareCallableLoci 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 Inputs
--comp1	NA	First comparison track name
--comp2	NA	Second comparison track name
Optional Outputs
--out -o	stdout	An output file created by the walker. Will overwrite contents if file exists
Optional Parameters
--printstate -printState	NA	If provided, prints sites satisfying this state pair

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.

--comp1 / -comp1

First comparison track name

This argument supports reference-ordered data (ROD) files in the following formats: BED

R RodBinding[BEDFeature] NA

--comp2 / -comp2

Second comparison track name

This argument supports reference-ordered data (ROD) files in the following formats: BED

R RodBinding[BEDFeature] NA

--out / -o

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

PrintStream stdout

--printstate / -printState

If provided, prints sites satisfying this state pair

String NA