Beagle 5.5

https://faculty.washington.edu/browning/beagle/
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Beagle is a software package for phasing genotypes and imputing ungenotyped markers. Beagle version...
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### Display gprobsmetrics help

Source: https://faculty.washington.edu/browning/beagle_utilities/utilities.html

Access the built-in help documentation for the utility via the command line.

```bash
java -jar gprobsmetrics.jar help
```

--------------------------------

### Execute gprobsmetrics.jar

Source: https://faculty.washington.edu/browning/beagle_utilities/utilities.html

Run the utility from the command line by piping a Beagle v3 genotype probabilities file into the JAR and redirecting the output to a file.

```bash
cat [gprobs] | java -jar gprobsmetrics.jar > [out]
```

--------------------------------

### Execute Beagle Analysis Workflow

Source: https://faculty.washington.edu/browning/beagle/run.beagle.28Jun21.220.example

Downloads required JARs and VCF data, prepares reference and target files, and runs Beagle analysis with various input parameters.

```bash
#!/bin/bash
if [ ! -f beagle.28Jun21.220.jar ]; then
  echo
  echo "Downloading beagle.28Jun21.220.jar"
  wget http://faculty.washington.edu/browning/beagle/beagle.28Jun21.220.jar
fi

if [ ! -f bref3.28Jun21.220.jar ]; then
  echo
  echo "Downloading bref3.28Jun21.220.jar"
  wget http://faculty.washington.edu/browning/beagle/bref3.28Jun21.220.jar
fi

echo

if [ ! -f test.28Jun21.220.vcf.gz ]; then
    echo
    echo "*** Downloading some 1000 Genomes Project data to file: test.28Jun21.220.vcf.gz ***"
    wget http://faculty.washington.edu/browning/beagle/test.28Jun21.220.vcf.gz
fi

echo
echo "*** Creating test files: ref.28Jun21.220.vcf.gz target.28Jun21.220.vcf.gz ***"
echo
zcat test.28Jun21.220.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.28Jun21.220.vcf.gz
zcat test.28Jun21.220.vcf.gz | cut -f1-9,191-200 | gzip > target.28Jun21.220.vcf.gz

echo
echo "*** Running test analysis with \"gt=\" argument ***"
echo
java -jar beagle.28Jun21.220.jar gt=test.28Jun21.220.vcf.gz out=out.gt

echo
echo "*** Running test analysis with \"ref=\" and \"gt=\" arguments ***"
echo
java -jar beagle.28Jun21.220.jar ref=ref.28Jun21.220.vcf.gz gt=target.28Jun21.220.vcf.gz out=out.ref

echo
echo "*** Making \"bref3\" file ***"
echo
java -jar bref3.28Jun21.220.jar ref.28Jun21.220.vcf.gz > ref.28Jun21.220.bref3

echo
echo "*** Running test analysis with \"bref3\" file ***"
echo
java -jar beagle.28Jun21.220.jar ref=ref.28Jun21.220.bref3 gt=target.28Jun21.220.vcf.gz out=out.bref3
```

--------------------------------

### Download and Prepare Beagle r1399 Environment

Source: https://faculty.washington.edu/browning/beagle/run.beagle.r1399.example

Downloads the Beagle JAR file and sample VCF data, then creates reference and target VCF files using standard Unix utilities.

```bash
#!/bin/bash
if [ ! -f beagle.r1399.jar ]; then
  echo
  echo "Downloading beagle.r1399.jar"
  wget http://faculty.washington.edu/browning/beagle/beagle.r1399.jar
fi

echo
echo "*** Downloading some 1000 Genomes Project data to file: test.r1399.vcf.gz ***"
echo
wget http://faculty.washington.edu/browning/beagle/test.r1399.vcf.gz

echo
echo "*** Creating test files: ref.r1399.vcf.gz target.r1399.vcf.gz ***"
echo
zcat test.r1399.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.r1399.vcf.gz
zcat test.r1399.vcf.gz | cut -f1-9,191-200 | gzip > target.r1399.vcf.gz
```

--------------------------------

### Execute updategprobs.jar via Command Line

Source: https://faculty.washington.edu/browning/beagle_utilities/utilities.html

Use this command to pipe an input file into the utility and redirect the output to a new file.

```bash
cat [gprobs] | java -jar updategprobs.jar [markers] [replace] > [out]
```

--------------------------------

### Download and Run Beagle Analysis Script

Source: https://faculty.washington.edu/browning/beagle/run.beagle.18May20.d20.example

A comprehensive bash script to download dependencies, prepare test VCF files, and execute Beagle analysis using different input configurations.

```bash
#!/bin/bash
if [ ! -f beagle.18May20.d20.jar ]; then
  echo
  echo "Downloading beagle.18May20.d20.jar"
  wget http://faculty.washington.edu/browning/beagle/beagle.18May20.d20.jar
fi

if [ ! -f bref3.18May20.d20.jar ]; then
  echo
  echo "Downloading bref3.18May20.d20.jar"
  wget http://faculty.washington.edu/browning/beagle/bref3.18May20.d20.jar
fi

echo

if [ ! -f test.18May20.d20.vcf.gz ]; then
    echo
    echo "*** Downloading some 1000 Genomes Project data to file: test.18May20.d20.vcf.gz ***"
    wget http://faculty.washington.edu/browning/beagle/test.18May20.d20.vcf.gz
fi

echo
echo "*** Creating test files: ref.18May20.d20.vcf.gz target.18May20.d20.vcf.gz ***"
echo
zcat test.18May20.d20.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.18May20.d20.vcf.gz
zcat test.18May20.d20.vcf.gz | cut -f1-9,191-200 | gzip > target.18May20.d20.vcf.gz

echo
echo "*** Running test analysis with \"gt=\" argument ***"
echo
java -jar beagle.18May20.d20.jar gt=test.18May20.d20.vcf.gz out=out.gt

echo
echo "*** Running test analysis with \"ref=\" and \"gt=\" arguments ***"
echo
java -jar beagle.18May20.d20.jar ref=ref.18May20.d20.vcf.gz gt=target.18May20.d20.vcf.gz out=out.ref

echo
echo "*** Making \"bref3\" file ***"
echo
java -jar bref3.18May20.d20.jar ref.18May20.d20.vcf.gz > ref.18May20.d20.bref3

echo
echo "*** Running test analysis with \"bref3\" file ***"
echo
java -jar beagle.18May20.d20.jar ref=ref.18May20.d20.bref3 gt=target.18May20.d20.vcf.gz out=out.bref3
```

--------------------------------

### Run base2genetic.jar

Source: https://faculty.washington.edu/browning/beagle_utilities/utilities.html

Converts base positions to genetic map positions by interpolating data from a provided map file.

```bash
usage: cat [input file] | java -jar base2genetic.jar [column] [map file] > [output file]
```

--------------------------------

### Execute Beagle Analysis Commands

Source: https://faculty.washington.edu/browning/beagle/run.beagle.r1399.example

Runs the Beagle JAR with different input arguments for genotype (gt), genotype likelihood (gl), and reference-based (ref) analysis.

```bash
echo
echo "*** Running test analysis with \"gt=\" argument ***"
echo
java -jar beagle.r1399.jar gt=test.r1399.vcf.gz out=out.gt

echo
echo "*** Running test analysis with \"gl=\" argument ***"
echo
java -jar beagle.r1399.jar gl=test.r1399.vcf.gz out=out.gl

echo
echo "*** Running test analysis with \"ref=\" argument ***"
echo
java -jar beagle.r1399.jar ref=ref.r1399.vcf.gz gt=target.r1399.vcf.gz out=out.ref
```

--------------------------------

### Run Beagle 29Oct24 Analysis Workflow

Source: https://faculty.washington.edu/browning/beagle/run.beagle.29Oct24.c8e.example

A bash script that downloads necessary JAR files, prepares test data, and executes Beagle analysis commands.

```bash
#!/bin/bash
if [ ! -f beagle.29Oct24.c8e.jar ]; then
  echo
  echo "Downloading beagle.29Oct24.c8e.jar"
  wget http://faculty.washington.edu/browning/beagle/beagle.29Oct24.c8e.jar
fi

if [ ! -f bref3.29Oct24.c8e.jar ]; then
  echo
  echo "Downloading bref3.29Oct24.c8e.jar"
  wget http://faculty.washington.edu/browning/beagle/bref3.29Oct24.c8e.jar
fi

echo

if [ ! -f test.29Oct24.c8e.vcf.gz ]; then
    echo
    echo "*** Downloading some 1000 Genomes Project data to file: test.29Oct24.c8e.vcf.gz ***"
    wget http://faculty.washington.edu/browning/beagle/test.29Oct24.c8e.vcf.gz
fi

echo
echo "*** Creating test files: ref.29Oct24.c8e.vcf.gz target.29Oct24.c8e.vcf.gz ***"
echo
zcat test.29Oct24.c8e.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.29Oct24.c8e.vcf.gz
zcat test.29Oct24.c8e.vcf.gz | cut -f1-9,191-200 | gzip > target.29Oct24.c8e.vcf.gz

echo
echo "*** Running test analysis with \"gt=\" argument ***"
echo
java -jar beagle.29Oct24.c8e.jar gt=test.29Oct24.c8e.vcf.gz out=out.gt

echo
echo "*** Running test analysis with \"ref=\" and \"gt=\" arguments ***"
echo
java -jar beagle.29Oct24.c8e.jar ref=ref.29Oct24.c8e.vcf.gz gt=target.29Oct24.c8e.vcf.gz out=out.ref

echo
echo "*** Making \"bref3\" file ***"
echo
java -jar bref3.29Oct24.c8e.jar ref.29Oct24.c8e.vcf.gz > ref.29Oct24.c8e.bref3

echo
echo "*** Running test analysis with \"bref3\" file ***"
echo
java -jar beagle.29Oct24.c8e.jar ref=ref.29Oct24.c8e.bref3 gt=target.29Oct24.c8e.vcf.gz out=out.bref3
```

--------------------------------

### Run consensusvcf.jar

Source: https://faculty.washington.edu/browning/beagle_utilities/utilities.html

Generates a consensus VCF file from multiple phased input VCF files using a majority vote.

```bash
usage: java -jar consensusvcf.jar [vcf 1] [vcf 2] ... > [consensus]
```

--------------------------------

### Bash script for Beagle subsample imputation

Source: https://faculty.washington.edu/browning/beagle/divide.sample

This script requires cut.jar, paste.jar, and beagle.jar. Ensure the variables for sample, reference, and markers are correctly defined before execution.

```bash
#!/bin/bash
#
# bash unix shell script for dividing a sample into subsamples and 
# performing imputation with Beagle on each subsample separately.
#
# paste.jar and cut.jar programs are available from the BEAGLE Utilities web page
# (http://www.stat.auckland.ac.nz/~bbrowning/beagle_utilities/utilities.html)

sample="?"	# replace ? with name of sample Beagle file
ref="?"		# replace ? with name of reference panel Beagle file
missing="?"	# replace ? with missing allele code
markers="?"	# replace ? with name of markers file with markers in reference panel

sampleCol="?"	# replace ? with number of columns (including first two columns) in sample Beagle file
windowSize="?"	# replace ? of number of columns of allele data to use per subsample (e.g. 500)

start="3"
let "end=start+windowSize-1"
z="10"

while [ "${end}" -lt "${sampleCol}" ]
do
  echo "start=${start}  end=${end}  subsample.index=${z}"
  cat ${sample} | java -jar cut.jar 1:2 ${start}:${end} > ${sample}.${z}
  java -jar beagle.jar phased=${ref} unphased=${sample}.${z} missing=${missing} markers=${markers} out=out.${z}
  let "start=end+1"
  let "end=start+windowSize-1"
  let "z=z+1"
done

echo "start=${start}  end=${sampleCol}  subsample.index=${z}"
cat ${sample} | java -jar cut.jar 1:2 ${start}:${sampleCol} > ${sample}.${z}
java -jar beagle.jar phased=${ref} unphased=${sample}.${z} missing=${missing} markers=${markers} out=out.${z}

java -jar paste.jar 2 out.[1-9][0-9].${sample}.[1-9][0-9].phased.gz | gzip > ${sample}.phased.gz
java -jar paste.jar 3 out.[1-9][0-9].${sample}.[1-9][0-9].gprobs.gz | gzip > ${sample}.gprobs.gz
java -jar paste.jar 3 out.[1-9][0-9].${sample}.[1-9][0-9].dose.gz | gzip > ${sample}.dose.gz
java -jar paste.jar 1 out.[1-9][0-9].${sample}.[1-9][0-9].r2 > ${sample}.r2
cat out.[1-9][0-9].log > ${sample}.log

rm ${sample}.[1-9][0-9]
rm out.[1-9][0-9].*
```

--------------------------------

### Calculate missing genotypes per sample

Source: https://faculty.washington.edu/browning/beagle_utilities/utilities.html

Calculates the proportion of uncalled genotypes for each sample in a Beagle v3 file based on a probability threshold.

```bash
usage: cat [gprobs] | java -jar gprobssamplemissing.jar [threshold] > [out]
```

--------------------------------

### Extract columns with cut.jar

Source: https://faculty.washington.edu/browning/beagle_utilities/utilities.html

Extracts specific columns from a white-space delimited file using column indices.

```bash
cat [input file] | java -jar cut.jar a1:b1 a2:b2 ... > [output file]
```

--------------------------------

### Calculate missing genotypes per marker

Source: https://faculty.washington.edu/browning/beagle_utilities/utilities.html

Calculates the proportion of uncalled genotypes for each marker in a Beagle v3 file based on a probability threshold.

```bash
usage: cat [gprobs] | java -jar gprobsmissing.jar [threshold] > [out]
```

--------------------------------

### Filter lines with filtercolumns.jar

Source: https://faculty.washington.edu/browning/beagle_utilities/utilities.html

Filters lines of input data based on numerical ranges or word matching in a specified field.

```bash
cat [input file] | java -jar filtercolumns.jar [line] [min] [max] > [output file]
```

```bash
cat [input file] | java -jar filtercolumns.jar [line] [word file] > [output file]
```
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