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concordance

Table of contents

  1. Description
  2. Usage
  3. Command line options
    1. Basic options
    2. Input parameters
    3. Other parameters
    4. Output files

Description

Program to compute the genotyping error rate at the sample or marker level.

Usage

Simple run

echo "chr20 ukb_white_british_sites.bcf validation_c20_snps.bcf imputed_ligated_c20_rp140k_1.0x.bcf" > concordance.txt

GLIMPSE2_concordance --gt-val --ac-bins 1 5 10 20 50 100 200 500 1000 2000 5000 10000  20000 50000 100000 140119 --threads 2 --input concordance.txt --output concordance_c20_rp140

Command line options

Basic options

Option name Argument Default Description
--help NA NA Produces help message
--seed INT 15052011 Seed of the random number generator
-T [ --threads ] INT 1 Number of threads

Input parameters

Option name Argument Default Description
--input FILE NA File with four columns listing in order: regions frequencies validation and imputed dataset. For genome-wide concordance, add more lines specifying different chromosomes.
--samples NA NA List of samples to process, one sample ID per line.
--gt-val NA NA Uses hard called genotypes rather than phread-scaled likelihoods for the validation dataset, reading them from FORMAT/GT field.
--gt-tar NA NA Uses FORMAT/GT field to determine the best-guess genotype rather than the FORMAT/GP (default). FORMAT/DS are FORMAT/GP fields are still required for calibration and rsquared calculations.

Other parameters

Option name Argument Default Description
--af-tag STRING AF Allele frequency INFO tag to use for binning. By default the allele frequency is estimated from the INFO/AF tag.
--use-alt-af NA NA If specified, the metrics work on the ALT allele frequency (range [0,1]), rather than minor allele frequency (range [0,0.5]).
--bins VECTOR NA Allele frequency bins used for rsquared computations. By default they should as MAF bins [0-0.5], while they should take the full range [0-1] if –use-ref-alt is used.
--ac-bins VECTOR NA User-defined allele count bins used for rsquared computations.
--allele-counts VECTOR NA Default allele count bins used for rsquared computations. AN field must be defined in the frequency file.
--min-val-gl FLOAT NA Minimum genotype likelihood probability P(G|R) in validation data [set to zero to have no filter of if using –gt-validation]
--min-val-dp INT NA Minimum coverage in validation data. If FORMAT/DP is missing and –minDP > 0, the program exits with an error. [set to zero to have no filter of if using –gt-validation]
--min-tar-gp VECTOR NA Minimum GP probabilities to be used as a filter. By default it looks at the GP field to specify the filter, but will try to use FORMAT/PL if gt-tar option is specified. Leave empty if no filter is used.
--out-r2-per-site NA NA Output r2 at each site.
--out-rej-sites NA NA Output sites where that cannot be used for the concordance.
--out-conc-sites NA NA Output sites where all target genotypes are concordant with the truth.
--out-disc-sites NA NA Output sites where at least one target genotype is diconcordant with the truth.
--groups FILE NA Alternative to frequency bins: group bins are user defined, provided in a file.

Output files

Option name Argument Default Description
-O [--output ] STRING NA Prefix of the output files (extensions are automatically added)
--log STRING NA Log file