REQUIRED for all errors and issues:
a) GATK version used: v4.4.0.0
b) Exact command used: GtcToVcf -INPUT 206307460092_R07C01.gtc -REFERENCE_SEQUENCE hg19_v0_Homo_sapiens_assembly19.fasta -OUTPUT 206307460092_R07C01.vcf -EXTENDED_ILLUMINA_MANIFEST /home/user3/Documents/ASA-24v1-0_E1.extended.csv -CLUSTER_FILE /home/user3/Documents/4th_Run.egt -ILLUMINA_BEAD_POOL_MANIFEST_FILE /home/user3/Documents/ASA-24v1-0_E1.bpm -SAMPLE_ALIAS my_sample_alias

c) Entire program log:

ava -jar /usr/local/picard.jar GtcToVcf INPUT=206307460092_R07C01.gtc REFERENCE_SEQUENCE=hg19_v0_Homo_sapiens_assembly19.fasta OUTPUT=206307460092_R07C01.vcf EXTENDED_ILLUMINA_MANIFEST=/home/user3/Documents/ASA-24v1-0_E1.extended.csv CLUSTER_FILE=/home/user3/Documents/4th_Run.egt ILLUMINA_BEAD_POOL_MANIFEST_FILE=/home/user3/Documents/ASA-24v1-0_E1.bpm SAMPLE_ALIAS=my_sample_alias
INFO    2023-03-29 13:22:25    GtcToVcf    

********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** 
https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
**********    GtcToVcf -INPUT 206307460092_R07C01.gtc -REFERENCE_SEQUENCE hg19_v0_Homo_sapiens_assembly19.fasta -OUTPUT 206307460092_R07C01.vcf -EXTENDED_ILLUMINA_MANIFEST /home/user3/Documents/ASA-24v1-0_E1.extended.csv -CLUSTER_FILE /home/user3/Documents/4th_Run.egt -ILLUMINA_BEAD_POOL_MANIFEST_FILE /home/user3/Documents/ASA-24v1-0_E1.bpm -SAMPLE_ALIAS my_sample_alias
**********

13:22:25.572 WARN  LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser
USAGE: GtcToVcf [options]

Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#GtcToVcf

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. 
(https://github.com/Illumina/BeadArrayFiles/blob/develop/docs/GTC_File_Format_v5.pdf) A VCF, aka Variant Calling Format,
is a text file for storing how a sequenced sample differs from the reference genome. 
(http://software.broadinstitute.org/software/igv/book/export/html/184)
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_BEAD_POOL_MANIFEST_FILE=chip_name.bpm \
SAMPLE_ALIAS=my_sample_alias \

Version: 3.0.0-1-g62ec81c-SNAPSHOT

Options:

--help
-h                            Displays options specific to this tool.

--stdhelp
-H                            Displays options specific to this tool AND options common to all Picard command line
                              tools.

--version                     Displays program version.

INPUT=File
I=File                        GTC file to be converted  Required. 

OUTPUT=File
O=File                        The output VCF file to write.  Required. 

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

CLUSTER_FILE=File
CF=File                       An Illumina cluster file (egt)  Required. 

ILLUMINA_BEAD_POOL_MANIFEST_FILE=File
BPM_FILE=File                 The Illumina Bead Pool Manifest (.bpm) file  Required. 

EXPECTED_GENDER=String
E_GENDER=String               The expected gender for this sample.  Default value: null. 

SAMPLE_ALIAS=String           The sample alias  Required. 

PIPELINE_VERSION=String       The version of the pipeline used to generate this VCF  Default value: null. 

ANALYSIS_VERSION_NUMBER=Integer
                              The analysis version of the data used to generate this VCF  Default value: null. 

GENDER_GTC=File
G_GTC=File                    An optional GTC file that was generated by calling the chip using a cluster file designed
                              to optimize gender calling.  Default value: null. 

FINGERPRINT_GENOTYPES_VCF_FILE=File
FP_VCF=File                   The fingerprint VCF for this sample  Default value: null. 

DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS=Boolean
                              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.  Default value: false. This option
                              can be set to 'null' to clear the default value. Possible values: {true, false} 

TMP_DIR=File                  One or more directories with space available to be used by this program for temporary
                              storage of working files  Default value: null. This option may be specified 0 or more
                              times. 

VERBOSITY=LogLevel            Control verbosity of logging.  Default value: INFO. This option can be set to 'null' to
                              clear the default value. Possible values: {ERROR, WARNING, INFO, DEBUG} 

QUIET=Boolean                 Whether to suppress job-summary info on System.err.  Default value: false. This option can
                              be set to 'null' to clear the default value. Possible values: {true, false} 

VALIDATION_STRINGENCY=ValidationStringency
                              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.  Default value: STRICT. This
                              option can be set to 'null' to clear the default value. Possible values: {STRICT, LENIENT,
                              SILENT} 

COMPRESSION_LEVEL=Integer     Compression level for all compressed files created (e.g. BAM and VCF).  Default value: 5.
                              This option can be set to 'null' to clear the default value. 

MAX_RECORDS_IN_RAM=Integer    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.  Default value: 500000.
                              This option can be set to 'null' to clear the default value. 

CREATE_INDEX=Boolean          Whether to create an index when writing VCF or coordinate sorted BAM output.  Default
                              value: false. This option can be set to 'null' to clear the default value. Possible
                              values: {true, false} 

CREATE_MD5_FILE=Boolean       Whether to create an MD5 digest for any BAM or FASTQ files created.    Default value:
                              false. This option can be set to 'null' to clear the default value. Possible values:
                              {true, false} 

REFERENCE_SEQUENCE=File
R=File                        Reference sequence file.  Required. 

USE_JDK_DEFLATER=Boolean
USE_JDK_DEFLATER=Boolean      Use the JDK Deflater instead of the Intel Deflater for writing compressed output  Default
                              value: false. This option can be set to 'null' to clear the default value. Possible
                              values: {true, false} 

USE_JDK_INFLATER=Boolean
USE_JDK_INFLATER=Boolean      Use the JDK Inflater instead of the Intel Inflater for reading compressed input  Default
                              value: false. This option can be set to 'null' to clear the default value. Possible
                              values: {true, false} 

OPTIONS_FILE=File             File of OPTION_NAME=value pairs.  No positional parameters allowed.  Unlike command-line
                              options, unrecognized options are ignored.  A single-valued option set in an options file
                              may be overridden by a subsequent command-line option.  A line starting with '#' is
                              considered a comment.  Required. 

The selected reference sequence ('true') is not supported.  This tool is currently only implemented to support NCBI Build 37 / HG19 Reference Sequence.