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GtcToVcf (Picard)

GtcToVcf takes an Illumina GTC file and converts it to a VCF file using several supporting files. A GTC file is an Illumina-specific file containing called genotypes in AA/AB/BB format. A VCF, aka Variant Calling Format, is a text file for storing how a sequenced sample differs from the reference genome.

Usage example:

java -jar picard.jar GtcToVcf \
INPUT=input.gtc \
REFERENCE_SEQUENCE=reference.fasta \
OUTPUT=output.vcf \
EXTENDED_ILLUMINA_MANIFEST=chip_name.extended.csv \
CLUSTER_FILE=chip_name.egt \
ILLUMINA_NORMALIZATION_MANIFEST=chip_name.bpm.csv \
SAMPLE_ALIAS=my_sample_alias \

Category Genotyping Arrays Manipulation


Overview

Class to convert a GTC file and a BPM file to a VCF file.

GtcToVcf (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
--CLUSTER_FILE
 -CF
null An Illumina cluster file (egt)
--EXTENDED_ILLUMINA_MANIFEST
 -MANIFEST
null An Extended Illumina Manifest file (csv). This is an extended version of the Illumina manifest it contains additional reference-specific fields
--ILLUMINA_NORMALIZATION_MANIFEST
 -NORM_MANIFEST
null An Illumina bead pool manifest (a manifest containing the Illumina normalization ids) (bpm.csv)
--INPUT
 -I
null GTC file to be converted
--OUTPUT
 -O
null The output VCF file to write.
--REFERENCE_SEQUENCE
 -R
null Reference sequence file.
--SAMPLE_ALIAS
null The sample alias
Optional Tool Arguments
--ANALYSIS_VERSION_NUMBER
null The analysis version of the data used to generate this VCF
--arguments_file
[] read one or more arguments files and add them to the command line
--DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS
false Causes the program to fail if it finds a case where there is a call on an assay that is flagged as 'zeroed-out' in the Illumina cluster file.
--EXPECTED_GENDER
 -E_GENDER
null The expected gender for this sample.
--FINGERPRINT_GENOTYPES_VCF_FILE
 -FP_VCF
null The fingerprint VCF for this sample
--GENDER_GTC
 -G_GTC
null An optional GTC file that was generated by calling the chip using a cluster file designed to optimize gender calling.
--help
 -h
false display the help message
--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 a BAM index when writing a coordinate-sorted BAM file.
--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.
--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.


--ANALYSIS_VERSION_NUMBER / NA

The analysis version of the data used to generate this VCF

Integer  null


--arguments_file / NA

read one or more arguments files and add them to the command line

List[File]  []


--CLUSTER_FILE / -CF

An Illumina cluster file (egt)

R File  null


--COMPRESSION_LEVEL / NA

Compression level for all compressed files created (e.g. BAM and VCF).

int  5  [ [ -∞  ∞ ] ]


--CREATE_INDEX / NA

Whether to create a BAM index when writing a coordinate-sorted BAM file.

Boolean  false


--CREATE_MD5_FILE / NA

Whether to create an MD5 digest for any BAM or FASTQ files created.

boolean  false


--DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS / NA

Causes the program to fail if it finds a case where there is a call on an assay that is flagged as 'zeroed-out' in the Illumina cluster file.

boolean  false


--EXPECTED_GENDER / -E_GENDER

The expected gender for this sample.

String  null


--EXTENDED_ILLUMINA_MANIFEST / -MANIFEST

An Extended Illumina Manifest file (csv). This is an extended version of the Illumina manifest it contains additional reference-specific fields

R File  null


--FINGERPRINT_GENOTYPES_VCF_FILE / -FP_VCF

The fingerprint VCF for this sample

File  null


--GA4GH_CLIENT_SECRETS / NA

Google Genomics API client_secrets.json file path.

String  client_secrets.json


--GENDER_GTC / -G_GTC

An optional GTC file that was generated by calling the chip using a cluster file designed to optimize gender calling.

File  null


--help / -h

display the help message

boolean  false


--ILLUMINA_NORMALIZATION_MANIFEST / -NORM_MANIFEST

An Illumina bead pool manifest (a manifest containing the Illumina normalization ids) (bpm.csv)

R File  null


--INPUT / -I

GTC file to be converted

R File  null


--MAX_RECORDS_IN_RAM / NA

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

The output VCF file to write.

R File  null


--QUIET / NA

Whether to suppress job-summary info on System.err.

Boolean  false


--REFERENCE_SEQUENCE / -R

Reference sequence file.

R File  null


--SAMPLE_ALIAS / NA

The sample alias

R String  null


--showHidden / -showHidden

display hidden arguments

boolean  false


--TMP_DIR / NA

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 / NA

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 / NA

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 / NA

display the version number for this tool

boolean  false


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GATK version 4.1.3.0 built at Fri, 9 Aug 2019 21:16:03 -0400.