CountBases

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

Category Diagnostics and Quality Control Tools

Traversal ReadWalker

PartitionBy READ

Overview

Input

One or more BAM files.

Output

Number of bases seen.

Examples

 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T CountBases \
   -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 CountBases.

MalformedReadFilter

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.