CalculateContamination

Calculate the fraction of reads coming from cross-sample contamination

Category Diagnostics and Quality Control

Overview

Calculates the fraction of reads coming from cross-sample contamination, given results from GetPileupSummaries. The resulting contamination table is used with FilterMutectCalls.

This tool is featured in the Somatic Short Mutation calling Best Practice Workflow. See Tutorial#11136 for a step-by-step description of the workflow and Article#11127 for an overview of what traditional somatic calling entails. For the latest pipeline scripts, see the Mutect2 WDL scripts directory.

This tool and GetPileupSummaries together replace GATK3's ContEst. Like ContEst, this tool estimates contamination based on the signal from ref reads at hom alt sites. However, ContEst uses a probabilistic model that assumes a diploid genotype with no copy number variation and independent contaminating reads. That is, ContEst assumes that each contaminating read is drawn randomly and independently from a different human. This tool uses a simpler estimate of contamination that relaxes these assumptions. In particular, it works in the presence of copy number variations and with an arbitrary number of contaminating samples. In addition, this tool is designed to work well with no matched normal data. However, one can run GetPileupSummaries on a matched normal bam file and input the result to this tool.

Usage examples

Tumor-only mode

 gatk CalculateContamination \
   -I pileups.table \
   -O contamination.table

Matched normal mode

 gatk CalculateContamination \
   -I tumor-pileups.table \
   -matched normal-pileups.table \
   -O contamination.table

The resulting table provides the fraction contamination, one line per sample, e.g. SampleID--TAB--Contamination. The file has no header.

CalculateContamination 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 Arguments
--input -I	null	The input table
--output -O	null	The output table
Optional Tool Arguments
--arguments_file	[]	read one or more arguments files and add them to the command line
--gcs-max-retries -gcs-retries	20	If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--help -h	false	display the help message
--high-coverage-ratio-threshold	3.0	The maximum coverage relative to the mean.
--low-coverage-ratio-threshold	0.5	The minimum coverage relative to the median.
--matched-normal -matched	null	The matched normal input table
--tumor-segmentation -segments	null	The output table containing segmentation of the tumor by minor allele fraction
--version	false	display the version number for this tool
Optional Common Arguments
--gatk-config-file	null	A configuration file to use with the GATK.
--QUIET	false	Whether to suppress job-summary info on System.err.
--TMP_DIR	[]	Undocumented option
--use-jdk-deflater -jdk-deflater	false	Whether to use the JdkDeflater (as opposed to IntelDeflater)
--use-jdk-inflater -jdk-inflater	false	Whether to use the JdkInflater (as opposed to IntelInflater)
--verbosity	INFO	Control verbosity of logging.
Advanced Arguments
--showHidden	false	display hidden arguments

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.