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=20Caveates
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 contigsPseudoAutosomal 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:
- 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.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 |
Input VCF or BCF with genotypes. | ||
--OUTPUT -O |
Output metrics file. | ||
--TRIOS -PED |
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 -PAR |
[X:154931044-155260560, X:60001-2699520, chrX:10001-2781479, chrX:155701383-156030895] | 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 |
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 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
--FEMALE_CHROMS
List of possible names for female sex chromosome(s)
Set[String] [chrX, X]
--GA4GH_CLIENT_SECRETS
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
List of possible names for male sex chromosome(s)
Set[String] [chrY, Y]
--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 [ [ -∞ ∞ ] ]
--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 / -PAR
List of chr:start-end for pseudo-autosomal regions on the female sex chromosome. Defaults to HG19/b37 & HG38 coordinates.
Set[String] [X:154931044-155260560, X:60001-2699520, chrX:10001-2781479, chrX:155701383-156030895]
--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
--SKIP_CHROMS
List of chromosome names to skip entirely.
Set[String] [MT, chrM]
--TAB_MODE
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
The number of threads that will be used to collect the metrics.
int 1 [ [ -∞ ∞ ] ]
--TMP_DIR
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
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
If provided, output per-family VCFs of mendelian violations into this directory.
File null
--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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