CountReads

Walks over the input data set, calculating the number of reads seen for diagnostic purposes.

Category Diagnostics and Quality Control Tools

Traversal ReadWalker

PartitionBy READ

Overview

Can also count the number of reads matching a given criterion using read filters (see the --read-filter command line argument). Simplest example of a read-backed analysis.

Input

One or more BAM files.

Output

Number of reads seen.

Examples

 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T CountReads \
   -I input.bam \
   [-L input.intervals]

Additional Information

Read filters

This Read Filter is automatically applied to the data by the Engine before processing by CountReads.

MalformedReadFilter

Parallelism options

This tool can be run in multi-threaded mode using this option.

NanoSchedulable (-nct)

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).

CommandLineGATK

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.