DrawPed: Documentation

DrawPed is a light-weight web tool for drawing human pedigrees and pedigree charts on the fly. You can also use pedigree files in PED format: Upload a PED file or download your finished pedigree file and pedigree chart for sharing or later use. You can use DrawPed programmatically and for batch jobs by using our API.

FAQs | Tutorial | Comparison with other tools | Source code

Documentation: Create a pedigree | Modify a pedigree | Save / export / share | API | Limitations | Licence

Create a pedigree

Here you can paste or upload a PED file or start drawing your pedigree from scratch.

Start with an existing pedigree

Upload PED file:

If you have an existing file in the pedigree format, and want to create a pedigree chart, choose the file under upload file and click on upload. DrawPed accepts plain text files with the file endings .ped, .pro and .txt.

Copy & paste:

You can also copy & paste a PED-formatted pedigree into the text field under pedigree or write a PED-formatted pedigree from scratch and click on send when done.

File format:

DrawPed accepts pedigrees without the first column denoting the family name and with an additional column starting with a # denoting special cases as in the DrawPed text field on the editing page. This is how pedigrees are displayed in the pedigree.

Multi-family files:

If your pedigree file contains more than one family, you will be asked to select one of the families. If you would like to draw multiple pedigree charts without having to click through the graphical user interface multiple times, consider using our API.

Use a template

We provide several links to sample pedigrees under start from template. These will take you directly to a complete DrawPed pedigree chart, which you can then edit.

Start from scratch

If you would like to start drawing from scratch, you can do so by creating a small nuclear family under create simple pedigree. Start by putting in a short identifier for the family, the Family ID. Write a short identifier or name for the index patient into the text field next to Index patient ID. Note that IDs must not contain empty spaces and should be kept rather short to still be readable in the pedigree chart.
Then select the role of the index patient in your nuclear family. It may be either daughter, son, father or mother. You can now enter the number of direct female daughters/sisters and male relatives sons/brothers.
If you have declared the index patient as a daughter or son, the number of relatives you put in will be the siblings. If you have declared the index patient as a father or mother, the number of relatives you put in will be the offspring.
Note that you have to put in at least one positive number into one of the fields, otherwise the pedigree will be empty and cannot be drawn by DrawPed.
Once you have filled in these fields, click create family.
You can add more relatives later on - this is just the initial pedigree that will be drawn by DrawPed.

Modify a pedigree

After putting in the pedigree information or uploading a file, you will now see the pedigree in the PED file format and the pedigree chart.

Pedigree chart

We mostly use the pedigree nomenclature defined by guidelines introduced by the National Society of Genetic Counseling Pedigree Task Force (see Bennett et al.) with the following deviations:

• Persons with an unknown affection will have an unfilled symbol, but with a blue instead of a black border.
• Miscarriage is represented as a small, crossed out symbol.

For an explanation of the symbols we use in the pedigree chart, please click here.

You may hide the IDs from the pedigree chart by switching on hide IDs to simplify or anonymise the output.
While you are editing the chart, we recommend displaying the IDs to avoid confusion.

Write into the PED text field

If you are familiar with the PED file format, you can directly make changes in the pedigree file text field and click apply changes to see the result.
Note that the since the family ID is the same for the whole family, it is not displayed inside the text field, but in a seperate field called Family ID. Therefore all columns are shifted to the left with respect to the usual pedigree format.

Use the graphical user interface options

When you click on a person in the pedigree chart, a menu appears. To close the menu without changing anything, click anywhere else on the page.
To make changes to the person you have clicked on, we provide several options:

Change sex	Use the radio buttons to change the sex of the individual to male, female or unknown sex. This option corresponds to changes in the 4th column in the text field containing the pedigree. Note that the sex of persons in a mating may not be changed.
Change affection	Use the radio buttons to change the status of the individual to affected, unaffected or unknown affection. This option corresponds to changes in the 5th column in the text field containing the pedigree. Note that unknown affection is marked as an unfilled shape with a blue border.
Change proband status	Use the checkbox to mark the individual as a proband/consultand or remove this mark. An arrow will appear on the left below this person. Note that we do not enforce that a proband must be affected. Therefore the better fitting term would be consultand (as proposed by Bennett et al.). However, since proband is the more commonly used term, we still use it in our interface.
Change deceased status	Use the checkbox to mark the individual as deceased or remove this mark. The person will be crossed out in the pedigree.
Change miscarriage status	Use the checkbox to mark the individual as a miscarriage. The symbol of the indidual will appear smaller and crossed out. Since a miscarriage implies death, a person should not be marked as deceased and a miscarriage. Miscarriages may obviously not have offspring themselves.
Change consanguineous status of parents	Use the checkbox to mark the parents of the clicked individual as consanguineous or remove this mark. All children of the parents will be marked. You may click on any of the children of a pair to add or remove this mark. A double line will appear between the parents. Using this option to mark a consanguineous union in the pedigree chart is only necessary if it is not apparent from the pedigree that the mates are related.
Change name	Change the individual ID, which is the display name of the person you have clicked. A dialog window will open, where you can put in the new name. Do not use whitespaces in the name. Press confirm to apply the change. All occurrences of the name will be changed; this means that the first three columns are affected by these changes. If you have added relatives with the given option, their names may be changed as well (e.g. when renaming testname, c_testname will also be changed).
Delete	Delete the individual from the pedigree. This is only possible, if the person does not have children. Children must be deleted before their parents. If the deleted individual has a parent, who does not have other children or parents themself, they will be automatically deleted as well. If you would like to delete multiple individuals at once, it may be faster to delete the lines in the pedigree text field.
Add parents	Add parents for this individual, if it does not have any already. The parents will be called f_[ID of individual] and m_[ID of individual].
Add child	Add a child of this individual to the pedigree. A dialog will open asking you for the sex of the child. If the individual has more than one partner, another dialog will open afterwards, asking you for the parent of the new child. The child will be called c_[ID of individual]. If this name already exists, a suffix will be added to the name (_[2..9]). Note that this option is only available, when the individual has at least one partner already.
Add child and partner	Add a child with a new partner to the pedigree. The partner will be called partner_[ID of individual]. Note that this option is only available, when the individual has fewer than two partners.
Add sibling	Add a sibling of this individual to the pedigree. A dialog will open asking you for the sex of the sibling. The sibling will be called s_[ID of individual]. If this name already exists, a suffix will be added to the name (_[2..9]). Note that the individual needs to have parents before it is possible to add siblings.

Save / export / share your pedigree

You can save your pedigree in the PED file format and the pedigree chart as an image or create a permalink to return to your DrawPed pedigree later. You can also collaborate on the pedigree with your colleagues.
Before saving the pedigree file, please fill in the family name. Otherwise, the files will be called FAM.[svg|png|ped].
You can anonymise the pedigree chart by checking hide IDs - this will remove the IDs from the plot.
These are the available options to save your pedigree:

🔗 Permalink	You can bookmark this link to resume work later or to share the pedigree with others.
👥 Collaborate	Collaborating allows you to work on a pedigree together by sharing a unique link with your colleagues. Please note: The PED file will be stored on our server, and anyone with the link can edit it. Ensure that only one person edits at a time to prevent data loss. Consider also saving the permalink to the pedigree to be able to revert changes. To see changes made by your collaborators, you must reload the page. We do however recommend to not work simultaneously on the same pedigree to avoid overwriting intended changes. Stored pedigrees must not contain any names. Collaboration links expire automatically after 7 days of inactivity (no edits), at which point the PED file is deleted from our servers. For an earlier deletion, use the button at the bottom of the page.
💾 SVG	Download the pedigree chart as a scalable vector graphic (SVG). Use this format for high-quality graphics, e.g. for publications.
💾 PNG	Download the pedigree chart in PNG format. PNG is a raster-based format and does not scale very well. Use this format to open pedigree charts in (older) applications unable to read SVG.
💾 PED file	Download the pedigree as text in the standard pedigree PED format. Use this format if you want to perform linkage analysis or with other applications such as PLINK.
💾 DrawPed file	Download the pedigree file with the flags that provide extra information to DrawPed which cannot be stored in the traditional pedigree format (e.g. about consanguinity, these are the words after the # at the end of a line). Note that these flags might cause problems when using other tools.

Application programming interface (API)

Whilst we do not provide a real API, it is simple to create pedigree charts automatically from a PED file. Use the command line command below to get a pedigree chart as an SVG file for a given pedigree.

Create a chart for a single-family PED file

curl -F svg=1 -F pedfile=@family.ped https://www.genecascade.org/ped-cgi/pedigree.cgi > family.svg	

The curl command will only work with single-family pedigree files.

Create charts for multi-family PED files

We provide a perl script to process multi-family files (see our example Perl script and a sample multi-family PED file). The script will produce an SVG file for each family contained in the PED file.

perl svg_from_pedfile.pl multifam.ped

Open a pedigree (including the pedigree chart) in DrawPed

If you plan to create simple hyperlinks or access using GET, you must perform URI encoding of the pedigree like so:

<!DOCTYPE HTML>
<html>
	<body>
	<form action="javascript:encode()" name="form1">
		<textarea name="example_ped">
			M1	0	0	2	1
			F1	GF1	GM1	1	2
			GM1	0	0	2	1
			GF1	0	0	1	1
			S1	F1	M1	2	2
			S2	F1	M1	1	1
		</textarea><br>
		<input type="submit"><br>
		<div id="hyperlink"></div>
	</form>
	<script>
		function encode () {
			document.getElementById("hyperlink").innerHTML=
				'https://www.genecascade.org/ped-cgi/pedigree.cgi?pedigree='
				+encodeURIComponent(document.form1.example_ped.value);
		}
	</script>
</body>
</html>

Limitations

Missing symbols and text in the chart

DrawPed does not currently draw the symbols to denote twins, adoptions, assisted reproduction, carriers of autosomal recessive and X-linked conditions, infertility/partners without children or breaks in the relationship line indicating the relationship no longer exists.
DrawPed also currently only displays one trait per pedigree. Changing this would be easy to implement though, please drop an email should you require this feature.
The text below a symbol is only used to display the ID of the person. It is not possible to additionally denote age, evaluation results (of genome sequencing, karyotyping etc.) or gender differing from sex assigned birth.

Charts, which cannot be drawn

DrawPed can detect consanguinity in a pedigree and mark these relationships with a double line, however, we cannot show recurrent parents yet.
Pedigrees producing overlapping lines in the pedigree chart such as multi-consanguineous families and more than two partners also cannot be drawn yet.

Licence

DrawPed is licensed under CC BY-SA 4.0 and free to use (including commercial use).
If you use pedigrees generated by DrawPed in a publication or use the code in your applications, you must cite Schönberger J, Steinhaus R, Seelow D. Drawing human pedigree charts with DrawPed. Nucleic Acids Research. 2024 May 10.
The source code is freely available at https://git-ext.charite.de/genecascade/DrawPed.