Laboratory of Dr. Tychele N. Turner, Ph.D.

Washington University in St. Louis

PYRUS

PYRUS is a tool for plotting copy number estimate data, from an individual, for user-specified regions of the genome. It has several options including plotting other individuals in the same region, plotting an annotation track, and writing out specific regions where the individuals have a copy number below or above given values. The input to the tool are bgzipped and tabix indexed bed files, which enables rapid plotting of the data.

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Get Started

Example Files:

Example With Example Directory

Example With Default Settings

Example With RefSeq Bed File

Example With Trio Family

Plot Together Example

Example With AUTS2 Bed File and Large Directory(not given)

Clone the PYRUS repository:

git clone https://github.com/TNTurnerLab/PYRUS.git

Running Pyrus Local Requirements

Users have the option to run PYRUS using Docker, or via the command line using Rscript.

The following R packages are required to run PYRUS:

• optparse
• dplyr
• seqminer
• data.table

Running on local command line with R:

Rscript /path/to/cloned/Repo/PYRUS.R -f /path/to/input/file/My_Bed_File.bed.gz -c /path/to/input/file/My_Chr_file.bed.gz {INSERT ANY MORE FLAGS IF NECESSARY}

Running Pyrus with Docker:

Pull the following Docker image:

docker pull tnturnerlab/pyrus

Run Docker image :

docker run -v /path/to/working/directory:/path/to/working/directory/ -w /path/to/cloned/Repo/ -it tnturnerlab/pyrus Rscript /path/to/cloned/Repo/PYRUS/PYRUS.R -f /path/to/input/file/My_Bed_File.bed.gz -c /path/to/input/file/My_Chr_file.bed.gz {INSERT ANY MORE FLAGS IF NECESSARY}

To run on LSF with Docker:

bsub -G name -q name -R 'rusage[mem=20GB]' -a 'docker(tnturnerlab/pyrus)' LC_ALL=C.UTF-8 Rscript /path/to/cloned/Repo/PYRUS/PYRUS.R /path/to/input/file/My_Bed_File.bed.gz -c /path/to/input/file/My_Chr_file.bed.gz {INSERT ANY MORE FLAGS IF NECESSARY}

File Requirements

• bgzipped and tabix-indexed bed files are the only acceptable file types for this script. For more information about how to prepare these files see bgzip and tabix

An example of the input bed file prior to bgzipping and tabix indexins is shown below:

chr1	0	54484	1.394791
chr1	54484	60739	1.258411
chr1	60739	68902	1.155175
chr1	68902	82642	2.633766

Required Flags :

-f :

Input the initial/main bgzipped and tabix indexed copy number estimate bed file for the individual

• default=NULL
• Ex: -f bedFile.bed.gz

-c :

Input a bgzipped and tabix indexed chromosome coordinate file containing the regions for plotting with PYRUS.

• default=NULL
• Ex: myChrbedfile.bed.gz

Optional Flags:

-o :

Enables the user to combine all plots into one PDF with user-specified name, the default setting is to plot each coordinate to its own PDF file

• default=NULL
• ex: -o multiplePagePDFFileofMyPlots.pdf

-r :

Flag to change the outputs from a pdf file to a low resolution png file.

• default=NULL
• Ex: -r y

-l :

Input a color for the line(s) created from the file given to the -f flag.

• default=blue,red
• Ex: -l blue,red

-y :

To change the sample name in the legend for the file specified with the -f argument. The default name will always be the first 15 characters of the filename.

• default=NULL
• Ex: -y MyNewName

-u:

Change the ylim maximum value for the plot window. The default is a copy number of 6.

• default=6
• Ex: -u 7

-d :

Input the directory path to bgzipped and tabix indexed bed files from additional samples. This option is used when the user wants to plot multiple samples. Note: the program will automatically search for .tbi files and requires them to run.

• default=NULL

• Ex: -d /path/to/a/directory/with/bed/file

  -s: 
  Flag used if user would like to plot every file in the given directory 
  against the file denoted by the -f flag. Must be used along with the -d flag.
  default=NULL	Ex: -d /path/to/dir/ -s y
  
  -p: 
  
  Input an ending pattern for files found inside the directory in "-d" flag. Must be the 
  ending pattern of the file. Can also be used to specify a specific file from a directory.
  
  default=.bed.gz	Ex: -d /path/to/dir/ -p .t1.cn.bed.gz	Ex: -d /path/to/dir/ -p exact.t1.cn.bed.gz 
  

-a :

Flag used if user would like to add an annotation track (e.g., exons) using a bgzipped and tabix indexed bed file. The default color settings for the annotation track included a red fill, black border, and Exon as the name,

• default=NULL

• ex: -a exonbedfile.bed

  -n: 
  
  Flag must be used along with "-a" to change the fill,boarder, and name of annotation track. 
  
  default=NULL	Ex: -a exonbedfile.bed.gz -n "color,color,name"
  

-b:

This flag will create a box-plot window in the top right corner of the existing line plot. The box plot will display the individual, marked with the -f flag, with a blue dot. This will automatically turn on if there are more than 10 files when multiplotting.

• default=NULL
• Ex: -b y

-t:

This flag takes two names, found in the chromosome coordinate file, and plots them side by side on a single plot. The two names must be from regions on the same chromosome. Data from the fourth column of the chromosome bed file must be used, typically it is a name/identifier. The default colors of these lines are blue and red, but can be modified with the -l flag.

• default=NULL
• Ex: -t BARX1,BARX1-DT

-g:

Threshold values for printing out names that are below the first value or above the second value. Note that if the user specificies the individual is male (-x M), the threshold for the X and Y chromosomes will be 1 less than the values indicated with this option.

• default="1.3,2.7"
• Ex: -g 2,3

-x:

If the sex is known for the individual in the file specified with the -f flag enter the value with this option. Default is F. This flag only has to be called if user wants to change sex to M.

• default=F
• Ex: -x M

-v:

Plot only the regions whose threshold values are below the first value of -g flag, or above the second of the -g flag. Note that the X and Y chromosomes will have a threshold one less than the values given if the sex is male.

• default=NULL
• Ex: -v y

-t:

Use this flag if intrested in plotting trios. Child file should be called with the -f flag, while parents should be called with the -j flag sepreated by ",".

• default=NULL
• Ex: -t /path/to/parent/1/file1.bed.gz,/path/to/parent/2/file2.bed.gz

-w:

This flag is used when initial data is not human.

• default="F"
• Ex: -w T

EXAMPLES

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Example With AUTS2 Bed File and Sample Directory

AUTS2_Sample_Directory.png

Rscript /Path/To/PYRUS/PYRUS.R -f /Path/To/PYRUS/Example_Data/WTC-11_Sample/WTC-11.bed.gz -c /Path/To/PYRUS/Example_Data/Sample_Reference_Data/AUTS2.bed -a /Path/To/PYRUS/Example_Data/Sample_Annotation_Track_Data/Exons.bed.gz  -d /Path/To/PYRUS/Example_Data/Sample_Database_Directory -o AUTS2_Sample_Directory.pdf -l dodgerblue -y WTC-11

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Example With Default Settings

Basic_Example.pdf

Rscript /Path/To/PYRUS/PYRUS.R -f /Path/To/PYRUS/Example_Data/WTC-11_Sample/WTC-11.bed.gz -c /Path/To/PYRUS/Example_Data/Sample_Reference_Data/AUTS2.bed -o Basic_Example.pdf

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Example With RefSeq Bed File

RefSeq.pdf

RefSeq_46XY_WTC-11.bed.gz_chromosomal_positions_outside_of_1.3_and_2.7.txt

Rscript /Path/To/PYRUS/PYRUS.R -f /Path/To/PYRUS/Example_Data/WTC-11_Sample/WTC-11.bed.gz -c /Path/To/PYRUS/Example_Data/Sample_Reference_Data/RefSeq.bed.gz -l dodgerblue -o RefSeq.pdf

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Example With Trio Family

TRIO_Family_NA12878.pdf

TRIO:46XX_NA12878.qm2.CN.1k.bed.gz_chromosomal_positions_outside_of_1.3_and_2.7.txt

Rscript /Path/To/PYRUS/PYRUS.R -f /Path/To/PYRUS/Example_Data/Example_Family/NA12878.qm2.CN.1k.bed.gz -c /Path/To/PYRUS/Example_Data/Sample_Reference_Data/Mills_et_al_2011_hg38_supplementary_table_s5_41586_2011_BFnature09708_MOESM246_ESM_simple_table_NA12878.bed -j /Path/To/PYRUS/Example_Data/Example_Family/NA12891.qm2.CN.1k.bed.gz,/Path/To/PYRUS/Example_Data/Example_Family/NA12892.qm2.CN.1k.bed.gz -a /Path/To/PYRUS/Example_Data/Sample_Annotation_Track_Data/Exons.bed.gz -l dodgerblue -o Trio_Family_NA12878.pdf

Trio_With_Directory.pdf

Rscript /Path/To/PYRUS/PYRUS.R -f /Path/To/PYRUS/Example_Data/Example_Family/NA12878.qm2.CN.1k.bed.gz -c /Path/To/PYRUS/Example_Data/Sample_Reference_Data/Zhang_et_al_2019_Table_S1_Standard_CNVs_pcbi.1007069.s004_successfully_lifted_to_hg38.bed -j /Path/To/PYRUS/Example_Data/Example_Family/NA12891.qm2.CN.1k.bed.gz,/Path/To/PYRUS/Example_Data/Example_Family/NA12892.qm2.CN.1k.bed.gz -a /Path/To/PYRUS/Example_Data/Sample_Annotation_Track_Data/Exons.bed.gz -d /Path/To/PYRUS/Example_Data/Sample_Database_Directory -l dodgerblue -o Trio_With_Directory.pdf

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Plot Together Example

Plot_Together_Example.pdf

Rscript /Path/To/PYRUS/PYRUS.R -f /Path/To/PYRUS/Example_Data/WTC-11_Sample/WTC-11.bed.gz -c /Path/To/PYRUS/Example_Data/Sample_Reference_Data/RefSeq.bed.gz -d /Path/To/PYRUS/Example_Data/Sample_Database_Directory -a /Path/To/PYRUS/Example_Data/Sample_Annotation_Track_Data/Exons.bed.gz -t BARX1,BARX-DT -o Plot_Together_Example.pdf

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Example With AUTS2 Bed File and Large Directory(not given)

AUTS2_Large_Directory_Example.pdf

Rscript /Path/To/PYRUS/PYRUS.R -f /Path/To/PYRUS/Example_Data/WTC-11_Sample/WTC-11.bed.gz -c /Path/To/PYRUS/Example_Data/Sample_Reference_Data/AUTS2.bed -a /Path/To/PYRUS/Example_Data/Sample_Annotation_Track_Data/Exons.bed.gz  -d /My/Large/Directory -o AUTS2_Sample_Directory.pdf -l dodgerblue -y WTC-11