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FindMendelianViolations (Picard)

Takes in VCF or BCF and a pedigree file and looks for high confidence calls where the genotype of the offspring is incompatible with the genotypes of the parents. Key features: - Checks for regular MVs in diploid regions and invalid transmissions in haploid regions (using the declared gender of the offspring in the pedigree file to determine how to deal with the male and female chromosomes.) - Outputs metrics about the different kinds of MVs found. - Can output a per-trio VCF with violations; INFO field will indicate the type of violation in the MV field

Example

java -jar picard.jar FindMendelianViolations\ I=input.vcf \ TRIO=pedigree.fam \ O=report.mendelian_violation_metrics \ MIN_DP=20

Caveates

Assumptions

The tool assumes the existence of FORMAT fields AD, DP, GT, GQ, and PL.

Ignored Variants

This tool ignores variants that are: - Not SNPs - Filtered - Multiallelic (i.e., trio has more than 2 alleles) - Within the SKIP_CHROMS contigs

PseudoAutosomal Region

This tool assumes that variants in the PAR will be mapped onto the female chromosome, and will treat variants in that region as as autosomal. The mapping to female requires that the PAR in the male chromosome be masked so that the aligner maps reads to single contig. This is normally done for the public releases of the human reference. The tool has default values for PAR that are sensible for humans on either build b37 or hg38.

Category Variant Evaluation and Refinement


Overview

Summary

Finds mendelian violations (MVs) of all types within a VCF.

Detail

Takes in VCF or BCF and a pedigree file and looks for high confidence calls where the genotype of the offspring is incompatible with the genotypes of the parents.
Key features:
  1. Checks for regular MVs in diploid regions and invalid transmissions in haploid regions (using the declared gender of the offspring in the pedigree file to determine how to deal with the male and female chromosomes.)
  2. Outputs metrics about the different kinds of MVs found
  3. Can output a per-trio VCF with violations; INFO field will indicate the type of violation in the MV field

Example

     java -jar picard.jar FindMendelianViolations\\
          I=input.vcf \\
          TRIO=pedigree.fam \\
          O=report.mendelian_violation_metrics \\
          MIN_DP=20
 

Caveates

Assumptions

The tool assumes the existence of FORMAT fields AD, DP, GT, GQ, and PL.

Ignored Variants

This tool ignores variants that are:
  • Not SNPs
  • Filtered
  • Multiallelic (i.e., trio has more than 2 alleles)
  • Within the #SKIP_CHROMS contigs

PseudoAutosomal Region

This tool assumes that variants in the PAR will be mapped onto the female chromosome, and will treat variants in that region as as autosomal. The mapping to female requires that the PAR in the male chromosome be masked so that the aligner maps reads to single contig. This is normally done for the public releases of the human reference. The tool has default values for PAR that are sensible for humans on either build b37 or hg38.

FindMendelianViolations (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
--INPUT
 -I
null Input VCF or BCF with genotypes.
--OUTPUT
 -O
null Output metrics file.
--TRIOS
 -PED
null File of Trio information in PED format (with no genotype columns).
Optional Tool Arguments
--arguments_file
[] read one or more arguments files and add them to the command line
--FEMALE_CHROMS
[chrX, X] List of possible names for female sex chromosome(s)
--help
 -h
false display the help message
--MALE_CHROMS
[chrY, Y] List of possible names for male sex chromosome(s)
--MIN_DP
 -DP
0 Minimum depth in each sample to consider possible mendelian violations.
--MIN_GQ
 -GQ
30 Minimum genotyping quality (or non-ref likelihood) to perform tests.
--MIN_HET_FRACTION
 -MINHET
0.3 Minimum allele balance at sites that are heterozygous in the offspring.
--PSEUDO_AUTOSOMAL_REGIONS
[chrX:10000-2781479, X:10001-2649520, chrX:155701382-156030895, X:59034050-59373566] List of chr:start-end for pseudo-autosomal regions on the female sex chromosome. Defaults to HG19/b37 & HG38 coordinates.
--SKIP_CHROMS
[MT, chrM] List of chromosome names to skip entirely.
--TAB_MODE
false If true then fields need to be delimited by a single tab. If false the delimiter is one or more whitespace characters. Note that tab mode does not strictly follow the PED spec
--THREAD_COUNT
1 The number of threads that will be used to collect the metrics.
--VCF_DIR
null If provided, output per-family VCFs of mendelian violations into this directory.
--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.


--arguments_file / NA

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

List[File]  []


--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


--FEMALE_CHROMS / NA

List of possible names for female sex chromosome(s)

Set[String]  [chrX, X]


--GA4GH_CLIENT_SECRETS / NA

Google Genomics API client_secrets.json file path.

String  client_secrets.json


--help / -h

display the help message

boolean  false


--INPUT / -I

Input VCF or BCF with genotypes.

R File  null


--MALE_CHROMS / NA

List of possible names for male sex chromosome(s)

Set[String]  [chrY, Y]


--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  [ [ -∞  ∞ ] ]


--MIN_DP / -DP

Minimum depth in each sample to consider possible mendelian violations.

int  0  [ [ -∞  ∞ ] ]


--MIN_GQ / -GQ

Minimum genotyping quality (or non-ref likelihood) to perform tests.

int  30  [ [ -∞  ∞ ] ]


--MIN_HET_FRACTION / -MINHET

Minimum allele balance at sites that are heterozygous in the offspring.

double  0.3  [ [ -∞  ∞ ] ]


--OUTPUT / -O

Output metrics file.

R File  null


--PSEUDO_AUTOSOMAL_REGIONS / NA

List of chr:start-end for pseudo-autosomal regions on the female sex chromosome. Defaults to HG19/b37 & HG38 coordinates.

Set[String]  [chrX:10000-2781479, X:10001-2649520, chrX:155701382-156030895, X:59034050-59373566]


--QUIET / NA

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


--SKIP_CHROMS / NA

List of chromosome names to skip entirely.

Set[String]  [MT, chrM]


--TAB_MODE / NA

If true then fields need to be delimited by a single tab. If false the delimiter is one or more whitespace characters. Note that tab mode does not strictly follow the PED spec

boolean  false


--THREAD_COUNT / NA

The number of threads that will be used to collect the metrics.

int  1  [ [ -∞  ∞ ] ]


--TMP_DIR / NA

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

List[File]  []


--TRIOS / -PED

File of Trio information in PED format (with no genotype columns).

R File  null


--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


--VCF_DIR / NA

If provided, output per-family VCFs of mendelian violations into this directory.

File  null


--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.