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

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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	null	MAP file for the PED file.
--ORIGINAL_VCF  -VCF	null	The vcf containing the original autocall genotypes.
--OUTPUT  -O	null	The output VCF file to write with merged genotype calls.
--PED_FILE  -PED	null	PED file to be merged into VCF.
--ZCALL_THRESHOLDS_FILE  -ZCALL_T_FILE	null	The zcall thresholds file.
--ZCALL_VERSION	null	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 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.
--REFERENCE_SEQUENCE  -R	null	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.

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--arguments_file / NA

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

List[File]  []

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--COMPRESSION_LEVEL / NA

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

int  5  [ [ -∞  ∞ ] ]

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--CREATE_INDEX / NA

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

Boolean  false

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--CREATE_MD5_FILE / NA

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

boolean  false

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--GA4GH_CLIENT_SECRETS / NA

Google Genomics API client_secrets.json file path.

String  client_secrets.json

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--help / -h

display the help message

boolean  false

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--MAP_FILE / -MAP

MAP file for the PED file.

R File  null

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--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  [ [ -∞  ∞ ] ]

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--ORIGINAL_VCF / -VCF

The vcf containing the original autocall genotypes.

R File  null

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--OUTPUT / -O

The output VCF file to write with merged genotype calls.

R File  null

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--PED_FILE / -PED

PED file to be merged into VCF.

R File  null

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--QUIET / NA

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

Boolean  false

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--REFERENCE_SEQUENCE / -R

Reference sequence file.

File  null

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--TMP_DIR / NA

One or more directories with space available to be used by this program for temporary storage of working files

List[File]  []

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--USE_JDK_DEFLATER / -use_jdk_deflater

Use the JDK Deflater instead of the Intel Deflater for writing compressed output

Boolean  false

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--USE_JDK_INFLATER / -use_jdk_inflater

Use the JDK Inflater instead of the Intel Inflater for reading compressed input

Boolean  false

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--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

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--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

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--version / NA

display the version number for this tool

boolean  false

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--ZCALL_THRESHOLDS_FILE / -ZCALL_T_FILE

The zcall thresholds file.

R File  null

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--ZCALL_VERSION / -ZCALL_VERSION

The version of zcall used

R String  null

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GATK version 4.1.4.0-32-gd78fa91 built at Fri, 22 Nov 2019 15:24:27 -0500.