Examples of CountLoci

org.broadinstitute.gatk.tools.walkers.qc.CountLoci
Walks over the input data set, calculating the total number of covered loci for diagnostic purposes.
This is the simplest example of a locus walker.

Input

One or more BAM files.

Output

Number of loci traversed. If an output file name is provided, then the result will be written to that file. Otherwise it will be sent to standard console output.

Examples
```
 java -Xmx2g -jar GenomeAnalysisTK.jar \ -T CountLoci \ -R ref.fasta \ -I input.bam \ -o output.txt \ [-L input.intervals] 
```

Examples of org.broadinstitute.gatk.tools.walkers.qc.CountLoci

    @DataProvider(name = "GATKReportCreationTest")
    public Object[][] makeGATKReportCreationTest() {
        List<Object[]> tests = new ArrayList<Object[]>();


        final Walker readWalker = new CountReads();
        final Walker lociWalker = new CountLoci();
        final Walker rodWalker = new CountRODs();
        final Walker artWalker = new RunReportDummyActiveRegionWalker();


        final Exception noException = null;
        final Exception javaException = new IllegalArgumentException("javaException");

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Examples of CountLoci

Input

Output

Examples

Examples of org.broadinstitute.gatk.tools.walkers.qc.CountLoci