GenotypeConcordance (Picard) – GATK

Calculates the concordance between genotype data of one samples in each of two VCFs - one being considered the truth (or reference) the other being the call. The concordance is broken into separate results sections for SNPs and indels. Statistics are reported in three different files.

Summary

Details

This tool evaluates the concordance between genotype calls for a sample in different callsets where one is being considered as the "truth" (aka standard, or reference) and the other as the "call" that is being evaluated for accuracy. The Comparison can be restricted to a confidence interval which is typically used in order to enable proper assessment of False Positives and the False-Positive Rate (FPR).

Usage example

Compare two VCFs within a confidence region

java -jar picard.jar GenotypeConcordance \ CALL_VCF=input.vcf \ CALL_SAMPLE=sample_name \ O=gc_concordance.vcf \ TRUTH_VCF=truth_set.vcf \ TRUTH_SAMPLE=sample_in_truth \ INTERVALS=confident.interval_list \ MISSING_SITES_HOM_REF = true

Output Metrics:

Output metrics consists of GenotypeConcordanceContingencyMetrics, GenotypeConcordanceSummaryMetrics, and GenotypeConcordanceDetailMetrics. For each set of metrics, the data is broken into separate sections for SNPs and INDELs. Note that only SNP and INDEL variants are considered, MNP, Symbolic, and Mixed classes of variants are not included. - GenotypeConcordanceContingencyMetrics enumerate the constituents of each contingent in a callset including true-positive(TP), true-negative (TN), false-positive (FP), and false-negative (FN) calls. Seehttp://broadinstitute.github.io/picard/picard-metric-definitions.html#GenotypeConcordanceContingencyMetrics for more details. - GenotypeConcordanceDetailMetrics include the numbers of SNPs and INDELs for each contingent genotype as well as thenumber of validated genotypes. Seehttp://broadinstitute.github.io/picard/picard-metric-definitions.html#GenotypeConcordanceDetailMetrics for more details.- GenotypeConcordanceSummaryMetrics provide specific details for the variant caller performance on a callset including:values for sensitivity, specificity, and positive predictive values. Seehttp://broadinstitute.github.io/picard/picard-metric-definitions.html#GenotypeConcordanceSummaryMetrics for more details. Useful definitions applicable to alleles and genotypes: Truthset - A callset (typically in VCF format) containing variant calls and genotypes that have been cross-validatedwith multiple technologies e.g. Genome In A Bottle Consortium (GIAB) (https://sites.stanford.edu/abms/giab) TP - True-positives are variant sites that match against the truth-set FP - False-positives are reference sites miscalled as variant FN - False-negatives are variant sites miscalled as reference TN - True-negatives are correctly called as reference Validated genotypes - are TP sites where the exact genotype (HET or HOM-VAR) appears in the truth-set

VCF Output:

- The concordance state will be stored in the CONC_ST tag in the INFO field - The truth sample name will be "truth" and call sample name will be "call"

Category Variant Evaluation and Refinement

Overview

Summary

Calculates the concordance between genotype data of one sample in each of two VCFs - one being considered the truth (or reference) the other being the call. The concordance is broken into separate results sections for SNPs and indels. Satistics are reported in three different files.

Details

This tool evaluates the concordance between genotype calls for a sample in different callsets where one is being considered as the \"truth\" (aka standard, or reference) and the other as the \"call\" that is being evaluated for accuracy. The Comparison can be restricted to a confidence interval which is typically used in order to enable proper assessment of False Positives and the False-Positive Rate (FPR).

Usage example

Compare two VCFs within a confidence region

 java -jar picard.jar GenotypeConcordance \\
       CALL_VCF=input.vcf \\
       CALL_SAMPLE=sample_name \\
       O=gc_concordance.vcf \\
       TRUTH_VCF=truth_set.vcf \\
       TRUTH_SAMPLE=sample_in_truth \\
       INTERVALS=confident.interval_list \\
       MISSING_SITES_HOM_REF = true

Output Metrics:

GenotypeConcordanceContingencyMetrics enumerate the constituents of each contingent in a callset including true-positive (TP), true-negative (TN), false-positive (FP), and false-negative (FN) calls.
GenotypeConcordanceDetailMetrics include the numbers of SNPs and INDELs for each contingent genotype as well as the number of validated genotypes.
GenotypeConcordanceSummaryMetrics provide specific details for the variant caller performance on a callset including values for sensitivity, specificity, and positive predictive values.

Useful definitions applicable to alleles and genotypes:

Truthset - A callset (typically in VCF format) containing variant calls and genotypes that have been cross-validated with multiple technologies e.g. Genome In A Bottle Consortium (GIAB) (https://sites.stanford.edu/abms/giab)
TP - True-positives are variant sites that match against the truth-set
FP - False-positives are reference sites miscalled as variant
FN - False-negatives are variant sites miscalled as reference
TN - True-negatives are correctly called as reference
Validated genotypes - are TP sites where the exact genotype (HET or HOM-VAR) appears in the truth-set

VCF Output:

The concordance state will be stored in the CONC_ST tag in the INFO field
The truth sample name will be \"truth\" and call sample name will be \"call\"

GenotypeConcordance (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
--CALL_VCF -CV	null	The VCF containing the call sample
--OUTPUT -O	null	Basename for the three metrics files that are to be written. Resulting files will be .genotype_concordance_summary_metrics, .genotype_concordance_detail_metrics, and .genotype_concordance_contingency_metrics.
--TRUTH_VCF -TV	null	The VCF containing the truth sample
Optional Tool Arguments
--arguments_file	[]	read one or more arguments files and add them to the command line
--CALL_SAMPLE -CS	null	The name of the call sample within the call VCF. Not required if only one sample exists.
--help -h	false	display the help message
--IGNORE_FILTER_STATUS	false	Default is false. If true, filter status of sites will be ignored so that we include filtered sites when calculating genotype concordance.
--INTERSECT_INTERVALS	true	If true, multiple interval lists will be intersected. If false multiple lists will be unioned.
--INTERVALS	[]	One or more interval list files that will be used to limit the genotype concordance. Note - if intervals are specified, the VCF files must be indexed.
--MIN_DP	0	Genotypes below this depth will have genotypes classified as LowDp.
--MIN_GQ	0	Genotypes below this genotype quality will have genotypes classified as LowGq.
--MISSING_SITES_HOM_REF -MISSING_HOM	false	Default is false, which follows the GA4GH Scheme. If true, missing sites in the truth set will be treated as HOM_REF sites and sites missing in both the truth and call sets will be true negatives. Useful when hom ref sites are left out of the truth set. This flag can only be used with a high confidence interval list.
--OUTPUT_ALL_ROWS	false	If true, output all rows in detailed statistics even when count == 0. When false only output rows with non-zero counts.
--OUTPUT_VCF	false	Output a VCF annotated with concordance information.
--TRUTH_SAMPLE -TS	null	The name of the truth sample within the truth VCF. Not required if only one sample exists.
--USE_VCF_INDEX	false	If true, use the VCF index, else iterate over the entire VCF.
--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] []

--CALL_SAMPLE / -CS

The name of the call sample within the call VCF. Not required if only one sample exists.

String null

--CALL_VCF / -CV

The VCF containing the call sample

R File null

--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

--GA4GH_CLIENT_SECRETS / NA

Google Genomics API client_secrets.json file path.

String client_secrets.json

--help / -h

display the help message

boolean false

--IGNORE_FILTER_STATUS / NA

Default is false. If true, filter status of sites will be ignored so that we include filtered sites when calculating genotype concordance.

boolean false

--INTERSECT_INTERVALS / NA

If true, multiple interval lists will be intersected. If false multiple lists will be unioned.

boolean true

--INTERVALS / NA

One or more interval list files that will be used to limit the genotype concordance. Note - if intervals are specified, the VCF files must be indexed.

List[File] []

--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 / NA

Genotypes below this depth will have genotypes classified as LowDp.

int 0 [ [ -∞ ∞ ] ]

--MIN_GQ / NA

Genotypes below this genotype quality will have genotypes classified as LowGq.

int 0 [ [ -∞ ∞ ] ]

--MISSING_SITES_HOM_REF / -MISSING_HOM

Default is false, which follows the GA4GH Scheme. If true, missing sites in the truth set will be treated as HOM_REF sites and sites missing in both the truth and call sets will be true negatives. Useful when hom ref sites are left out of the truth set. This flag can only be used with a high confidence interval list.

boolean false

--OUTPUT / -O

Basename for the three metrics files that are to be written. Resulting files will be .genotype_concordance_summary_metrics, .genotype_concordance_detail_metrics, and .genotype_concordance_contingency_metrics.

R File null

--OUTPUT_ALL_ROWS / NA

If true, output all rows in detailed statistics even when count == 0. When false only output rows with non-zero counts.

boolean false

--OUTPUT_VCF / NA

Output a VCF annotated with concordance information.

boolean false

--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

--TMP_DIR / NA

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

List[File] []

--TRUTH_SAMPLE / -TS

The name of the truth sample within the truth VCF. Not required if only one sample exists.

String null

--TRUTH_VCF / -TV

The VCF containing the truth sample

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

--USE_VCF_INDEX / NA

If true, use the VCF index, else iterate over the entire VCF.

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

--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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Articles in this section

Summary

Details

Usage example

Compare two VCFs within a confidence region

Output Metrics:

VCF Output:

Category Variant Evaluation and Refinement

Overview

Summary

Details

Usage example

Compare two VCFs within a confidence region

Output Metrics:

VCF Output:

GenotypeConcordance (Picard) specific arguments

Argument details

--arguments_file / NA

--CALL_SAMPLE / -CS

--CALL_VCF / -CV

--COMPRESSION_LEVEL / NA

--CREATE_INDEX / NA

--CREATE_MD5_FILE / NA

--GA4GH_CLIENT_SECRETS / NA

--help / -h

--IGNORE_FILTER_STATUS / NA

--INTERSECT_INTERVALS / NA

--INTERVALS / NA

--MAX_RECORDS_IN_RAM / NA

--MIN_DP / NA

--MIN_GQ / NA

--MISSING_SITES_HOM_REF / -MISSING_HOM

--OUTPUT / -O

--OUTPUT_ALL_ROWS / NA

--OUTPUT_VCF / NA

--QUIET / NA

--REFERENCE_SEQUENCE / -R

--showHidden / -showHidden

--TMP_DIR / NA

--TRUTH_SAMPLE / -TS

--TRUTH_VCF / -TV

--USE_JDK_DEFLATER / -use_jdk_deflater

--USE_JDK_INFLATER / -use_jdk_inflater

--USE_VCF_INDEX / NA

--VALIDATION_STRINGENCY / NA

--VERBOSITY / NA

--version / NA