CollectArraysVariantCallingMetrics (Picard)

CollectArraysVariantCallingMetrics takes a Genotyping Arrays VCF file (as generated by GtcToVcf) and calculates summary and per-sample metrics.

Usage example:

java -jar picard.jar CollectArraysVariantCallingMetrics \
      INPUT=genotyping_arrays.vcf \
      OUTPUT=outputBaseName

Category Diagnostics and Quality Control

Overview

Collects summary and per-sample metrics about variant calls in a VCF file.

CollectArraysVariantCallingMetrics (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
--CALL_RATE_PF_THRESHOLD	0.98	The Call Rate Threshold for an autocall pass (if the observed call rate is > this value, the sample is considered to be passing)
--help -h	false	display the help message
--NUM_PROCESSORS	0	Split this task over multiple threads. If NUM_PROCESSORS = 0, number of cores is automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0 then the number of cores used will be the number available on the machine less NUM_PROCESSORS.
--SEQUENCE_DICTIONARY -SD		If present, speeds loading of dbSNP file, will look for dictionary in vcf if not present here.
--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.
--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] []

--CALL_RATE_PF_THRESHOLD

The Call Rate Threshold for an autocall pass (if the observed call rate is > this value, the sample is considered to be passing)

Double 0.98 [ [ -∞ ∞ ] ]

--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

--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 [ [ -∞ ∞ ] ]

--NUM_PROCESSORS

Split this task over multiple threads. If NUM_PROCESSORS = 0, number of cores is automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0 then the number of cores used will be the number available on the machine less NUM_PROCESSORS.

int 0 [ [ -∞ ∞ ] ]

--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.

PicardHtsPath 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

--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

Return to top

GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.