the buffer size for the samjdk.
the buffer size for the samjdk.
Looks up the first super class that does not have "$anon$" in its name.
Looks up the first super class that does not have "$anon$" in its name.
the compress level to use.
the compress level to use.
true if we are to create an index, false otherwise.
true if we are to create an index, false otherwise.
true if we are to create an Md5 file, false otherwise.
true if we are to create an Md5 file, false otherwise.
The path to the JAR to be executed.
The path to the JAR to be executed.
a list of arguments to the JVM.
a list of arguments to the JVM.
use advanced garbage collection parameters.
use advanced garbage collection parameters.
true if we are to use asynchronous IO, false otherwise.
true if we are to use asynchronous IO, false otherwise.
set the default validation stringency for Picard.
set the default validation stringency for Picard.
Sets asynchronous IO on or off.
Sets asynchronous IO on or off.
Sets the compression level to a specific value.
Sets the compression level to a specific value.
Sets asynchronous IO on or off.
Sets asynchronous IO on or off.
Runs Picard's GenotypeConcordance to assess various variant calling metrics against truth.
Please note MISSING_SITES_HOM_REF is set to true by default, whereas the default in GenotypeConcordance is false.