Updated Beagle walker for gatkdocs format. Pushed unsupported, undocumented arguments to @Hidden
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Guillermo del Angel
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40f64a27be
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671330950d
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@ -48,6 +48,31 @@ import static java.lang.Math.log10;
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/**
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* Takes files produced by Beagle imputation engine and creates a vcf with modified annotations.
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*
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* <p>This walker is intended to be run after Beagle has successfully executed. The full calling sequence for using Beagle along with the GATK is: </p>
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*
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* <p>1. Run ProduceBeagleInputWalker. </p>
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* <p>2. Run Beagle</p>
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* <p>3. Uncompress output files</p>
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* <p>4. Run BeagleOutputToVCFWalker.</p>
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*
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*
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* Note that this walker requires all input files produced by Beagle.
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*
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*
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* <h2>Example</h2>
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* <pre>
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* java -Xmx4000m -jar dist/GenomeAnalysisTK.jar \
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* -R reffile.fasta -T BeagleOutputToVCF \
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* -B:variant,VCF input_vcf.vcf \
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* -B:beagleR2,BEAGLE /myrun.beagle_output.r2 \
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* -B:beaglePhased,BEAGLE /myrun.beagle_output.phased \
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* -B:beagleProbs,BEAGLE /myrun.beagle_output.gprobs \
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* --out output_vcf.vcf
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* </pre>
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<p> Note that Beagle produces some of these files compressed as .gz, so gunzip must be run on them before walker is run in order to decompress them </p>
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*/
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public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
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@ -57,22 +82,18 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
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@Input(fullName="comp", shortName = "comp", doc="Comparison VCF file", required=false)
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public RodBinding<VariantContext> comp;
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@Input(fullName="beagleR2", shortName = "beagleR2", doc="VCF file", required=true)
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@Input(fullName="beagleR2", shortName = "beagleR2", doc="Beagle-produced .r2 file containing R^2 values for all markers", required=true)
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public RodBinding<BeagleFeature> beagleR2;
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@Input(fullName="beagleProbs", shortName = "beagleProbs", doc="VCF file", required=true)
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@Input(fullName="beagleProbs", shortName = "beagleProbs", doc="Beagle-produced .probs file containing posterior genotype probabilities", required=true)
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public RodBinding<BeagleFeature> beagleProbs;
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@Input(fullName="beaglePhased", shortName = "beaglePhased", doc="VCF file", required=true)
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@Input(fullName="beaglePhased", shortName = "beaglePhased", doc="Beagle-produced .phased file containing phased genotypes", required=true)
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public RodBinding<BeagleFeature> beaglePhased;
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@Output(doc="File to which variants should be written",required=true)
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@Output(doc="VCF File to which variants should be written",required=true)
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protected VCFWriter vcfWriter = null;
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@Argument(fullName="output_file", shortName="output", doc="Please use --out instead" ,required=false)
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@Deprecated
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protected String oldOutputArg;
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@Argument(fullName="dont_mark_monomorphic_sites_as_filtered", shortName="keep_monomorphic", doc="If provided, we won't filter sites that beagle tags as monomorphic. Useful for imputing a sample's genotypes from a reference panel" ,required=false)
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public boolean DONT_FILTER_MONOMORPHIC_SITES = false;
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@ -48,19 +48,45 @@ import java.io.PrintStream;
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import java.util.*;
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/**
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* Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input variant file
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* Converts the input VCF into a format accepted by the Beagle imputation/analysis program.
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* <p>
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*
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* <h2>Input</h2>
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* <p>
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* A VCF with variants to convert to Beagle format
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* </p>
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*
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* <h2>Outputs</h2>
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* <p>
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* A single text file which can be fed to Beagle
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* </p>
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* <p>
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* Optional: A file with a list of markers
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* </p>
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*
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* <h2>Examples</h2>
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* <pre>
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* java -Xmx2g -jar dist/GenomeAnalysisTK.jar -L 20 \
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* -R reffile.fasta -T ProduceBeagleInput \
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* -B:variant,VCF path_to_input_vcf/inputvcf.vcf -o path_to_beagle_output/beagle_output
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* </pre>
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*
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*/
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public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
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@ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
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@Input(fullName="validation", shortName = "validation", doc="Input VCF file", required=false)
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@Hidden
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@Input(fullName="validation", shortName = "validation", doc="Validation VCF file", required=false)
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public RodBinding<VariantContext> validation;
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@Output(doc="File to which BEAGLE input should be written",required=true)
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protected PrintStream beagleWriter = null;
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@Output(doc="File to which BEAGLE markers should be written", shortName="markers", fullName = "markers", required = false)
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@Hidden
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@Output(doc="File to which BEAGLE markers should be written", shortName="markers", fullName = "markers", required = false)
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protected PrintStream markers = null;
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int markerCounter = 1;
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@ -73,14 +99,19 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
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@Argument(doc="VQSqual key", shortName = "vqskey", required=false)
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protected String VQSLOD_KEY = "VQSqual";
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@Argument(fullName = "inserted_nocall_rate", shortName = "nc_rate", doc = "Rate (0-1) at which genotype no-calls will be randomly inserted, for testing", required = false)
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@Hidden
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@Argument(fullName = "inserted_nocall_rate", shortName = "nc_rate", doc = "Rate (0-1) at which genotype no-calls will be randomly inserted, for testing", required = false)
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public double insertedNoCallRate = 0;
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@Argument(fullName = "validation_genotype_ptrue", shortName = "valp", doc = "Flat probability to assign to validation genotypes. Will override GL field.", required = false)
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@Hidden
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@Argument(fullName = "validation_genotype_ptrue", shortName = "valp", doc = "Flat probability to assign to validation genotypes. Will override GL field.", required = false)
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public double validationPrior = -1.0;
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@Argument(fullName = "validation_bootstrap", shortName = "bs", doc = "Proportion of records to be used in bootstrap set", required = false)
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@Hidden
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@Argument(fullName = "validation_bootstrap", shortName = "bs", doc = "Proportion of records to be used in bootstrap set", required = false)
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public double bootstrap = 0.0;
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@Argument(fullName = "bootstrap_vcf",shortName = "bvcf", doc = "Output a VCF with the records used for bootstrapping filtered out", required = false)
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@Hidden
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@Argument(fullName = "bootstrap_vcf",shortName = "bvcf", doc = "Output a VCF with the records used for bootstrapping filtered out", required = false)
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VCFWriter bootstrapVCFOutput = null;
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@Argument(fullName = "checkIsMaleOnChrX", shortName = "checkIsMaleOnChrX", doc = "Set to true when Beagle-ing chrX and want to ensure male samples don't have heterozygous calls.", required = false)
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public boolean CHECK_IS_MALE_ON_CHR_X = false;
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