MergePedIntoVcf takes a single-sample ped file output from zCall and merges into a single-sample vcf file using several supporting files.A VCF, aka Variant Calling Format, is a text file for storing how a sequenced sample differs from the reference genome. A PED file is a whitespace-separated text file for storing genotype information. A MAP file is a whitespace-separated text file for storing information about genetic distance. A zCall thresholds file is a whitespace-separated text file for storing the thresholds for genotype clustering for a SNP as determined by zCall.
Usage example:
java -jar picard.jar MergePedIntoVcf \
VCF=input.vcf \
PED=zcall.output.ped \
MAP=zcall.output.map \
ZCALL_T_FILE=zcall.thresholds.7.txt \
OUTPUT=output.vcf
Category Genotyping Arrays Manipulation
Overview
Class to take genotype calls from a ped file output from zCall and merge them into a vcf from autocall.MergePedIntoVcf (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 | |||
--MAP_FILE -MAP |
MAP file for the PED file. | ||
--ORIGINAL_VCF -VCF |
The vcf containing the original autocall genotypes. | ||
--OUTPUT -O |
The output VCF file to write with merged genotype calls. | ||
--PED_FILE -PED |
PED file to be merged into VCF. | ||
--ZCALL_THRESHOLDS_FILE -ZCALL_T_FILE |
The zcall thresholds file. | ||
--ZCALL_VERSION |
The version of zcall used | ||
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
--MAP_FILE / -MAP
MAP file for the PED file.
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 [ [ -∞ ∞ ] ]
--ORIGINAL_VCF / -VCF
The vcf containing the original autocall genotypes.
R File null
--OUTPUT / -O
The output VCF file to write with merged genotype calls.
R File null
--PED_FILE / -PED
PED file to be merged into VCF.
R File null
--QUIET
Whether to suppress job-summary info on System.err.
Boolean false
--REFERENCE_SEQUENCE / -R
Reference sequence file.
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
--ZCALL_THRESHOLDS_FILE / -ZCALL_T_FILE
The zcall thresholds file.
R File null
--ZCALL_VERSION / -ZCALL_VERSION
The version of zcall used
R String null
GATK version 4.2.4.0-SNAPSHOT built at Thu, 16 Dec 2021 11:57:48 -0800.
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