# GenotypeConcordance

Genotype concordance (per-sample and aggregate counts and frequencies, NRD/NRS and site allele overlaps) between two callsets

## Overview

GenotypeConcordance takes in two callsets (vcfs) and tabulates the number of sites which overlap and share alleles, and for each sample, the genotype-by-genotype counts (e.g. the number of sites at which a sample was called homozygous-reference in the EVAL callset, but homozygous-variant in the COMP callset). It outputs these counts as well as convenient proportions (such as the proportion of het calls in the EVAL which were called REF in the COMP) and metrics (such as NRD and NRS).

### Input

Genotype concordance requires two callsets (as it does a comparison): an EVAL and a COMP callset, specified via the -eval and -comp arguments. Typically, the EVAL callset is an experimental set you want to evaluate, while the COMP callset is a previously existing set used as a standard for comparison (taken to represent "truth").

(Optional) Jexl expressions for genotype-level filtering of EVAL or COMP genotypes, specified via the -gfe and -cfe arguments, respectively.

### Output

Genotype Concordance writes a GATK report to the specified file (via -o), consisting of multiple tables of counts and proportions. These tables are constructed on a per-sample basis, and include counts of EVAL vs COMP genotype states.

#### Tables

Headers for the (non-moltenized -- see below) GenotypeConcordance counts and proportions tables give the genotype of the COMP callset followed by the genotype of the EVAL callset. For example the value corresponding to HOM_REF_HET reflects variants called HOM_REF in the COMP callset and HET in the EVAL callset. Variants for which the alternate alleles between the EVAL and COMP sample did not match are excluded from genotype comparisons and given in the "Mismatching_Alleles" field.

It may be informative to reshape rows of the GenotypeConcordance counts and proportions tables into separate row-major tables where the columns indicate the COMP genotype and the rows indicate the EVAL genotype for easy comparison between the two callsets. This can be done with a command similar to d <- matrix(sampleRow,nrow=6,byrow=T) in R where sampleRow is the 36-value row corresponding to the sample of interest, excluding "Mismatching_Alleles". In Excel this can be accomplished using the OFFSET function.

• GenotypeConcordance_CompProportions: Gives the proportion of variants in each category normalized to the total number of called genotypes in the COMP callset
• GenotypeConcordance_Counts: Gives the counts for number of genotypes in each category
• GenotypeConcordance_EvalProportions: Gives the proportion of genotypes in each category normalized to the total number of called genotypes in the EVAL callset
• GenotypeConcordance_Summary: Summary statistics for the sum of all samples and each sample individually. See below for definitions.
• SiteConcordance_Summary: Gives comparison counts of called genotypes and their alleles between the two callsets. See below for definitions.

#### Term and metrics definitions

• GenotypeConcordance_CompProportions, GenotypeConcordance_Counts, and GenotypeConcordance_EvalProportions
• NO_CALL: reported genotype is ./., indicating not enough data to call
• HET: heterozygous
• HOM_REF: homozygous reference
• HOM_VAR: homozygous variant
• UNAVAILABLE: variant is not called in this callset
• MIXED: something like ./1
• GenotypeConcordance_Summary
• Non-Reference_Sensitivity (NRS): sensitivity of the EVAL calls to polymorphic calls in the COMP set, calculated by (# true positive)/(# true polymorphic)
• Non-Reference_Discrepancy (NRD): genotype discordance excluding concordant reference sites, calculated by (# discordant sites)/(total excluding # HOM_REF_HOM_REF) = 1.0-(# HOM_VAR_HOM_VAR + # HET_HET)/(total excluding # HOM_REF_HOM_REF)
• Overall_Genotype_Concordance: overall concordance calculated by (# concordant genotypes)/(# genotypes)
• SiteConcordance_Summary
• ALLELES_MATCH: counts of calls at the same site where the alleles match
• ALLELES_DO_NOT_MATCH: counts of calls at the same location with different alleles, such as the EVAL set calling a 'G' alternate allele, and the comp set calling a 'T' alternate allele
• EVAL_SUBSET_TRUTH: (multi-alleleic sites only) ALT alleles for EVAL are a subset of ALT alleles for COMP. See also below.
• EVAL_SUPERSET_TRUTH: (multi-allelic sites only) ALT alleles for COMP are a subset of ALT alleles for EVAL. See also below.
• EVAL_ONLY: counts of sites present only in the EVAL set, not in the COMP set
• TRUTH_ONLY: counts of sites present only in the COMP set, not in the EVAL set

#### Site-level allelic concordance

For strictly bi-allelic VCFs, only the ALLELES_MATCH, EVAL_ONLY, TRUTH_ONLY fields will be populated, but where multi-allelic sites are involved counts for EVAL_SUBSET_TRUTH and EVAL_SUPERSET_TRUTH will be generated.

For example, in the following situation

    eval:  ref - A   alt - C
comp:  ref - A   alt - C,T

then the site is tabulated as EVAL_SUBSET_TRUTH. Were the situation reversed, it would be EVAL_SUPERSET_TRUTH. However, in the case where EVAL has both C and T alternate alleles, both must be observed in the genotypes (that is, there must be at least one of (0/1,1/1) and at least one of (0/2,1/2,2/2) in the genotype field). If one of the alleles has no observations in the genotype fields of the EVAL, the site-level concordance is tabulated as though that allele were not present in the record.

#### Monomorphic Records

A site which has an alternate allele, but which is monomorphic in samples, is treated as not having been discovered, and will be recorded in the TRUTH_ONLY column (if a record exists in the COMP set), or not at all (if no record exists in the COMP set).

That is, in the situation

   eval:  ref - A   alt - C   genotypes - 0/0  0/0  0/0 ... 0/0
comp:  ref - A   alt - C   ...         0/0  0/0  ...

is equivalent to
   eval:  ref - A   alt - .   genotypes - 0/0  0/0  0/0 ... 0/0
comp:  ref - A   alt - C   ...         0/0  0/0  ...


When a record is present in the COMP set the *genotypes* for the monomorphic site will still be used to evaluate per-sample genotype concordance counts.

#### Filtered Records

Filtered records are treated as though they were not present in the VCF, unless -ignoreSiteFilters is provided, in which case all records are used. There is currently no way to assess concordance metrics on filtered sites exclusively. SelectVariants can be used to extract filtered sites, and VariantFiltration used to un-filter them.

#### Moltenized tables

These tables may be optionally moltenized via the -moltenize argument. That is, the standard table

  Sample   NO_CALL_HOM_REF  NO_CALL_HET  NO_CALL_HOM_VAR   (...)
NA12878       0.003        0.001            0.000        (...)
NA12891       0.005        0.000            0.000        (...)

  NA12878  NO_CALL_HOM_REF   0.003
NA12878  NO_CALL_HET       0.001
NA12878  NO_CALL_HOM_VAR   0.000
NA12891  NO_CALL_HOM_REF   0.005
NA12891  NO_CALL_HET       0.000
NA12891  NO_CALL_HOM_VAR   0.000
(...)


These Read Filters are automatically applied to the data by the Engine before processing by GenotypeConcordance.

### Downsampling settings

This tool applies the following downsampling settings by default.

• Mode: BY_SAMPLE
• To coverage: 1,000

## Command-line Arguments

### Inherited arguments

The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).

### GenotypeConcordance 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 Inputs
--comp
NA The variants and genotypes to compare against
--eval
NA The variants and genotypes to evaluate
Required Flags
--moltenize
NA Molten rather than tabular output
Optional Outputs
--out
-o
NA An output file created by the walker. Will overwrite contents if file exists
Optional Parameters
--genotypeFilterExpressionComp
-gfc
NA One or more criteria to use to set COMP genotypes to no-call. These genotype-level filters are only applied to the COMP rod.
--genotypeFilterExpressionEval
-gfe
NA One or more criteria to use to set EVAL genotypes to no-call. These genotype-level filters are only applied to the EVAL rod.
--printInterestingSites
-sites
NA File to output the discordant sites and genotypes.
Optional Flags
--ignoreFilters
NA Filters will be ignored

### 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.

### --comp / -comp

The variants and genotypes to compare against
The callset you want to treat as 'truth'. Can also be of unknown quality for the sake of callset comparisons.

--comp binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3

R RodBinding[VariantContext]

### --eval / -eval

The variants and genotypes to evaluate
The callset you want to evaluate, typically this is where you'd put 'unassessed' callsets.

--eval binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3

R RodBinding[VariantContext]

### --genotypeFilterExpressionComp / -gfc

One or more criteria to use to set COMP genotypes to no-call. These genotype-level filters are only applied to the COMP rod.
Identical to -gfe except the filter is applied to genotypes in the comp rod.

ArrayList[String]

### --genotypeFilterExpressionEval / -gfe

One or more criteria to use to set EVAL genotypes to no-call. These genotype-level filters are only applied to the EVAL rod.
A genotype level JEXL expression to apply to eval genotypes. Genotypes filtered in this way will be replaced by NO_CALL. For instance: -gfe 'GQ<20' will set to no-call any genotype with genotype quality less than 20.

ArrayList[String]

### --ignoreFilters / NA

Filters will be ignored
The FILTER field of the eval and comp VCFs will be ignored. If this flag is not included, all FILTER sites will be treated as not being present in the VCF. (That is, the genotypes will be assigned UNAVAILABLE, as distinct from NO_CALL).

boolean

### --moltenize / -moltenize

Molten rather than tabular output
Moltenize the count and proportion tables. Rather than moltenizing per-sample data into a 2x2 table, it is fully moltenized into elements. That is, WITHOUT this argument, each row of the table begins with the sample name and proceeds directly with counts/proportions of eval/comp counts (for instance HOM_REF/HOM_REF, HOM_REF/NO_CALL). If the Moltenize argument is given, the output will begin with a sample name, followed by the contrastive genotype type (such as HOM_REF/HOM_REF), followed by the count or proportion. This will significantly increase the number of rows.

boolean

### --out / -o

An output file created by the walker. Will overwrite contents if file exists

PrintStream

### --printInterestingSites / -sites

File to output the discordant sites and genotypes.
Print sites where genotypes are mismatched between callsets along with annotations giving the genotype of each callset to the given filename

PrintStream