Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file.
Category Diagnostics and Quality Control
Overview
Collects summary and per-sample metrics about variant calls in a VCF file.CollectVariantCallingMetrics (Picard) 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 | |||
--DBSNP |
Reference dbSNP file in dbSNP or VCF format. | ||
--INPUT -I |
Input vcf file for analysis | ||
--OUTPUT -O |
Path (except for the file extension) of output metrics files to write. | ||
Optional Tool Arguments | |||
--arguments_file |
read one or more arguments files and add them to the command line | ||
--GVCF_INPUT |
false | Set to true if running on a single-sample gvcf. | |
--help -h |
false | display the help message | |
--SEQUENCE_DICTIONARY -SD |
If present, speeds loading of dbSNP file, will look for dictionary in vcf if not present here. | ||
--TARGET_INTERVALS -TI |
Target intervals to restrict analysis to. | ||
--THREAD_COUNT |
1 | Undocumented option | |
--version |
false | display the version number for this tool | |
Optional Common Arguments | |||
--COMPRESSION_LEVEL |
5 | Compression level for all compressed files created (e.g. BAM and VCF). | |
--CREATE_INDEX |
false | Whether to create an index when writing VCF or coordinate sorted BAM output. | |
--CREATE_MD5_FILE |
false | Whether to create an MD5 digest for any BAM or FASTQ files created. | |
--GA4GH_CLIENT_SECRETS |
client_secrets.json | Google Genomics API client_secrets.json file path. | |
--MAX_RECORDS_IN_RAM |
500000 | When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed. | |
--QUIET |
false | Whether to suppress job-summary info on System.err. | |
--REFERENCE_SEQUENCE -R |
Reference sequence file. | ||
--TMP_DIR |
One or more directories with space available to be used by this program for temporary storage of working files | ||
--USE_JDK_DEFLATER -use_jdk_deflater |
false | Use the JDK Deflater instead of the Intel Deflater for writing compressed output | |
--USE_JDK_INFLATER -use_jdk_inflater |
false | Use the JDK Inflater instead of the Intel Inflater for reading compressed input | |
--VALIDATION_STRINGENCY |
STRICT | Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. | |
--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.
--arguments_file
read one or more arguments files and add them to the command line
List[File] []
--COMPRESSION_LEVEL
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
--CREATE_INDEX
Whether to create an index when writing VCF or coordinate sorted BAM output.
Boolean false
--CREATE_MD5_FILE
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
--DBSNP
Reference dbSNP file in dbSNP or VCF format.
R File null
--GA4GH_CLIENT_SECRETS
Google Genomics API client_secrets.json file path.
String client_secrets.json
--GVCF_INPUT
Set to true if running on a single-sample gvcf.
boolean false
--help / -h
display the help message
boolean false
--INPUT / -I
Input vcf file for analysis
R File null
--MAX_RECORDS_IN_RAM
When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.
Integer 500000 [ [ -∞ ∞ ] ]
--OUTPUT / -O
Path (except for the file extension) of output metrics files to write.
R File null
--QUIET
Whether to suppress job-summary info on System.err.
Boolean false
--REFERENCE_SEQUENCE / -R
Reference sequence file.
File null
--SEQUENCE_DICTIONARY / -SD
If present, speeds loading of dbSNP file, will look for dictionary in vcf if not present here.
File null
--showHidden / -showHidden
display hidden arguments
boolean false
--TARGET_INTERVALS / -TI
Target intervals to restrict analysis to.
File null
--THREAD_COUNT
Undocumented option
int 1 [ [ -∞ ∞ ] ]
--TMP_DIR
One or more directories with space available to be used by this program for temporary storage of working files
List[File] []
--USE_JDK_DEFLATER / -use_jdk_deflater
Use the JDK Deflater instead of the Intel Deflater for writing compressed output
Boolean false
--USE_JDK_INFLATER / -use_jdk_inflater
Use the JDK Inflater instead of the Intel Inflater for reading compressed input
Boolean false
--VALIDATION_STRINGENCY
Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values:
- STRICT
- LENIENT
- SILENT
ValidationStringency STRICT
--VERBOSITY
Control verbosity of logging.
The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:
- ERROR
- WARNING
- INFO
- DEBUG
LogLevel INFO
--version
display the version number for this tool
boolean false
GATK version 4.2.4.0-SNAPSHOT built at Thu, 16 Dec 2021 11:57:48 -0800.
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