Write variant tensors for training a CNN to filter variants
gatk CNNVariantWriteTensors \ -R reference.fasta \ -V input.vcf.gz \ -truth-vcf platinum-genomes.vcf \ -truth-bed platinum-confident-region.bed \ -tensor-type reference \ -output-tensor-dir my-tensor-folder
gatk CNNVariantWriteTensors \ -R reference.fasta \ -V input.vcf.gz \ -truth-vcf platinum-genomes.vcf \ -truth-bed platinum-confident-region.bed \ -tensor-type read_tensor \ -bam-file input.bam \ -output-tensor-dir my-tensor-folder
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 | |||
--output-tensor-dir |
null | Directory of training tensors. Subdivided into train, valid and test sets. | |
--reference -R |
null | Reference fasta file. | |
--truth-bed |
null | Confident region of the validated VCF file. | |
--truth-vcf |
null | Validated VCF file. | |
--variant -V |
null | Input VCF file | |
Optional Tool Arguments | |||
--arguments_file |
[] | read one or more arguments files and add them to the command line | |
--bam-file |
"" | BAM or BAMout file to use for read data when generating 2D tensors. | |
--downsample-indels |
0.5 | Fraction of INDELs to write tensors for. | |
--downsample-snps |
0.05 | Fraction of SNPs to write tensors for. | |
--gcs-max-retries -gcs-retries |
20 | If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection | |
--gcs-project-for-requester-pays |
"" | Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. | |
--help -h |
false | display the help message | |
--max-tensors |
1000000 | Maximum number of tensors to write. | |
--tensor-type |
reference | Name of the tensors to generate. | |
--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 |
null | Temp directory to use. | |
--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 | |||
--annotation-set |
best_practices | Which set of annotations to use. | |
--channels-last |
true | Store the channels in the last axis of tensors, tensorflow->true, theano->false | |
--showHidden |
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.
Which set of annotations to use.
String best_practices
read one or more arguments files and add them to the command line
List[File] []
BAM or BAMout file to use for read data when generating 2D tensors.
String ""
Store the channels in the last axis of tensors, tensorflow->true, theano->false
boolean true
Fraction of INDELs to write tensors for.
float 0.5 [ [ -∞ ∞ ] ]
Fraction of SNPs to write tensors for.
float 0.05 [ [ -∞ ∞ ] ]
A configuration file to use with the GATK.
String null
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
int 20 [ [ -∞ ∞ ] ]
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.
String ""
display the help message
boolean false
Maximum number of tensors to write.
int 1000000 [ [ 0 ∞ ] ]
Directory of training tensors. Subdivided into train, valid and test sets.
R String null
Whether to suppress job-summary info on System.err.
Boolean false
Reference fasta file.
R String null
display hidden arguments
boolean false
Name of the tensors to generate.
The --tensor-type argument is an enumerated type (TensorType), which can have one of the following values:
TensorType reference
Temp directory to use.
GATKPathSpecifier null
Confident region of the validated VCF file.
R String null
Validated VCF file.
R String null
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
Input VCF file
R String null
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
LogLevel INFO
display the version number for this tool
boolean false
See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum
GATK version 4.1.4.0 built at Wed, 9 Oct 2019 15:19:59 -0400.