VcfToAdpc takes a VCF, as generated by GtcToVcf and generates an Illumina 'adpc.bin' file from it. An adpc.bin file is a binary file containing genotyping array intensity data that can be exported by Illumina's GenomeStudio and Beadstudio analysis tools. The adpc.bin file is used as an input to VerifyIDintensity a tool for detecting and estimating sample contamination of Illumina genotyping array data. If more than one VCF is used, they must all have the same number of loci.
Usage example:
java -jar picard.jar VcfToAdpc \
VCF=input.vcf \
OUTPUT=output.adpc.bin \
SAMPLES_FILE=output.samples.txt \
NUM_MARKERS_FILE=output.num_markers.txt \
Category Genotyping Arrays Manipulation
Overview
A simple program to convert a Genotyping Arrays VCF to an ADPC file (Illumina intensity data file).VcfToAdpc (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 | |||
--NUM_MARKERS_FILE -NMF |
A text file into which the number of loci in the VCF will be written. This is useful for calling verifyIDIntensity. | ||
--OUTPUT -O |
The output (adpc.bin) file to write. | ||
--SAMPLES_FILE -SF |
A text file into which the names of the samples will be written. These will be in the same order as the data in the adpc.bin file. | ||
--VCF |
One or more VCF files containing array intensity data. | ||
Optional Tool Arguments | |||
--arguments_file |
read one or more arguments files and add them to the command line | ||
--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 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
--GA4GH_CLIENT_SECRETS
Google Genomics API client_secrets.json file path.
String client_secrets.json
--help / -h
display the help message
boolean false
--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_MARKERS_FILE / -NMF
A text file into which the number of loci in the VCF will be written. This is useful for calling verifyIDIntensity.
R File null
--OUTPUT / -O
The output (adpc.bin) file 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
--SAMPLES_FILE / -SF
A text file into which the names of the samples will be written. These will be in the same order as the data in the adpc.bin file.
R 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
--VCF
One or more VCF files containing array intensity data.
R List[File] []
--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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