Calculate the fraction of reads coming from cross-sample contamination
The resulting contamination table is used with FilterMutectCalls.
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.
The resulting table provides the fraction contamination, one line per sample, e.g. SampleID--TAB--Contamination. The file has no header.
gatk CalculateContamination \ -I pileups.table \ -O contamination.table
gatk CalculateContamination \ -I tumor-pileups.table \ -matched normal-pileups.table \ -O contamination.table
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|
|null||The input table|
|null||The output table|
|Optional Tool Arguments|
||||read one or more arguments files and add them to the command line|
|20||If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection|
|false||display the help message|
||3.0||The maximum coverage relative to the mean.|
||0.5||The minimum coverage relative to the median.|
|null||The matched normal input table|
||false||display the version number for this tool|
|Optional Common Arguments|
||null||A configuration file to use with the GATK.|
||false||Whether to suppress job-summary info on System.err.|
|false||Whether to use the JdkDeflater (as opposed to IntelDeflater)|
|false||Whether to use the JdkInflater (as opposed to IntelInflater)|
||INFO||Control verbosity of logging.|
||false||display hidden arguments|
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.
read one or more arguments files and add them to the command line
A configuration file to use with the GATK.
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
int 20 [ [ -∞ ∞ ] ]
display the help message
The maximum coverage relative to the mean.
double 3.0 [ [ -∞ ∞ ] ]
The input table
R File null
The minimum coverage relative to the median.
double 0.5 [ [ -∞ ∞ ] ]
The matched normal input table
The output table
R File null
Whether to suppress job-summary info on System.err.
display hidden arguments
Whether to use the JdkDeflater (as opposed to IntelDeflater)
Whether to use the JdkInflater (as opposed to IntelInflater)
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
display the version number for this tool
GATK version 18.104.22.168 built at 10-58-2018 11:58:10.