User Manual Version 2.4 - Software Tools for Animal Gene Mapping
Contents
1. Pedigraph A Software Tool for the Graphing and Analysis of Large Complex Pedigree User Manual Version 2 4 INTERNET VERSION WITH LOWER GRAPHIC QUALITY JOHN R GARBE AND YANG DA DEPARTMENT OF ANIMAL SCIENCE UNIVERSITY OF MINNESOTA AUGUST 19 2008 INTRODUCTION cccscsssssssscscsscssesssscscssrcsscscsssssensssescssnssscscsssssasessescssnesacscsssesasesssaesassssencsscesasessenes 3 GELTTING STARTED cinis ieceres iiien eisein o ieaie os e tenei te 3 2 1 On Microsoft Windows 6 ec A Re A ee S 3 2 2 O E NC Oo i SO RO ee 3 INPUT FILES Ct a e a nia lidad liinda 3 3 1 Pedigree P11 6 secs sek O ieee a a we e Ee 4 3 2 Paraineter file sccseccccck sitet sees hack cxece ce Resta a e Rode o a a Wa deecdocetee ee E aa 5 3 3 ColOr definitlOMs dt Coasts oe Meee tebe 7 PEDIGREE DRAWING sacicesessccet soci eteeccecbuesiaceteisecse sisest Se i Soei iei a S 8 4 1 Full pedigree drawing with default settings sseessesessseseesseserssseesessteeesseseesseserseeseenesseseeses 8 4 2 Display of trait status LA a AEA 9 4 3 Color ECONO E A A Ali 10 NI E E E eee 11 4 5 Generations Sap itis ete tac O 11 4 6 Tests for drawing full pedigrees of large complex populations oooooonccnnnnincnoonconnonnconnconocnnoo 12 4 7 Compact pedigree drawing using summary OptiOn ceeceeseceecseeesseeeeeeeeeeeeeereeeeneeeees 14 4 8 Comparison between compact and full pedigrees ceccescesseeseceteceseceeecseeeseeeseenseeneee2. A15 A21 JOQOE Figure 2 Full pedigree drawing with affected individuals highlighted in gold color Dam Sire Sire A B al a2 a3 a4 Css a6 a7 a8 al a2 a4 a5 a6 a7 Sire Sire C D al a2 a4 a5 a6 a7 al a2 a4 a5 a6 a7 Dam Sire Dam D Sire E F al a2 a3 a4 a5 a6 a7 a8 al a2 f a3 a4 a5 a6 a7 a8 Figure 3 Selected color options to highlight affected individuals in the pedigree drawing A affected 1 statement is used in pedigraph dat B affected 1 and affectedcolor green statements are used in pedigraph dat C affected 1 and affectedcolor blue statements are used in pedigraph dat D affected 1 and affectedcolor red statements are used in pedigraph dat E affected 1 and affectedcolor pink statements are used in pedigraph dat F affected 1 and affectedcolor tan statements are used in pedigraph dat 10 4 3 Color controls Colors of pedigree nodes are controlled by four options nocolor affectedcolor nodecolor and fillcolor The nocolor option draws a black white pedigree while the oth
3. familysize 2 will all families with at least two offspring in the pedigree drawing Figure 11 shows examples of pedigree drawing with minimal family size requirements lt a gt ar lt a gt Cia gets i as A9 A5 A19 A17 az a30 A25 A27 A B lt fr Paty A2 Te 3 gt yO A lt e g D gt a aa Ss Al7 A29 Cao A25 A27 A25 A27 A29 A30 C D Figure 14 Pedigree drawings with minimal family size requirement A Full pedigree B Minimal family size of 2 C Minimal family size of 3 D Minimal family size 0f 4 20 4 12 Page Controls Pedigraph offers a number of options to control page layout including pagewidth pageheight nomargin width height and title statements Table 1 For a large pedigree the pedigree drawing may be displayed on several pages under the default page size Increasing the page size using pagewidth and pageheight statements may achieve the goal to print the entire pedigree drawing on one page 5 INBREEDING COEFFICIENTS Pedigraph has a utility to calculate inbreeding coefficients The inbreeding coefficient of each individual can be displayed along with the individual s ID or be stored in a file 5 1 Display of inbreeding coefficients in pedigree drawing The inbreeding statement in pedigraph dat executes t
4. of Figure 8 the same summary principle is implemented but the offspring counts are represented in one node with four cells In comparison B is more compact than A but A has a regular pedigree appearance and is more artistic than B A B Figure 9 Compact pedigree drawings drawing with two offspring groupings A Offspring are grouped by gender B Offspring are grouped by gender and trait status Figure 9 shows compact pedigree drawing with two offspring groupings using the same pedigree data for drawing Figures 1 2 A summary 1 statement is added to the pedigraph dat used by Figure 1 This results in offspring grouping by gender only B summary 1 and affected 1 statements are added to the pedigraph dat used by Figures 1 This results in offspring grouping by gender and trait status 4 8 Comparison between compact and full pedigrees Comparisons between compact and full pedigrees of large complex populations are available from http animalgene umn edu For the unofficial European Royalty Genealogy Database with over 48 000 individuals spanning over 100 generations summary 1 reduced the pedigree size by about 2 3 For the swine melanoma population with about 2069 individuals in large families Figure 10 summary 1 reduced the pedigree size by about 95 i e the compa
5. of the individual s siblings following individual statement Draw the pedigree of the individual s ancestors following individual statement Print the pedigree data of the selected individual to a file The color used to indicate affected individuals The pedigree is drawn in black and white The color used to outline individual nodes The color used to indicate unaffected individuals Minimum number of offspring for a mating to be drawn A title to be printed on the drawing Display nodes for unknown individuals Distance in inches between generations rows of nodes Print progress information to the screen while the program is running Width in inches of the drawing Height in inches of the drawing Width in inches of a page e g 8 5 Height in inches of a page e g 11 Prevents margins on multi page drawings outputfile Jpg png output ps Name of the output file Create the output file in jpg format Supported on Windows only Create the output file in the png format instead of PostScript Supported on Windows only inbreeding inbreedfile coancestryfile coancestryoutputfile coancestry coancestryped output file name arrows title No coancestry calculation No output No coancestry calculation No arrows No title Turns on calculation of inbreeding coefficients Name of the file in which inbreeding coefficients will be printed Ifa file is not speci
6. pedigree drawing required 40 minutes of CPU time to print on a 2 GHz Pentium 4 desktop computer The size of the pedigree printout appears to be the only major limitation for pedigree drawing using Pedigraph A readable printout of the main body of the full pedigree could be as large as 100 feet wide and 80 feet tall Figure 7A The drawings gives a good sense of the overall structure of the full pedigree and reveals highly complex relationships a visual effect that is impossible from reading the genealogy data On the computer screen details of a small area of the full pedigree could be viewed clearly using zoom in Figure 7B Figure 7 Full pedigree drawing of the European Royal Genealogical Data A Main body of the full pedigree drawing omitting a long horizontal string at the top right B Zoom in of a small area of the full pedigree 13 4 7 Compact pedigree drawing using summary option Pedigraph has two summary options summary 1 and summary 2 for compact pedigree drawing These two summary options display parents and the number of offspring in each family The summary 1 option displays each offspring group in a separate node while the summary 2 option displays all offspring groups in each family in different cells of one node which yields more compact but less artistic pedigree drawing than summary 1 option A compact pedigree drawing can be much smaller than t
7. the executable with this command chmod u x pedigraph 3 INPUT FILES Pedigraph requires one input file the pedigree file containing pedigree information and an optional parameter file containing program options The parameter file must be named as pedigraph dat In the event pedigraph dat is missing or empty the pedigree is drawn using default options as described in 4 1 3 1 Pedigree file The data file is a simple text file that contains the pedigree to be drawn Each line gives the ID of an individual column 1 as well as the IDs of the individual s parents columns 2 and 3 the gender of the individual column 4 and optionally a trait status column 5 Individual ID s in column can be characters or numbers other than 0 zero Parental IDs in columns 2 and 3 can be characters or numbers A parental ID of 0 indicates an unknown parent The default gender code is M for males and F for females The user may use other gender codes using the male and female options in the parameter files Gender codes other than the default codes or the user specified codes are considered as missing gender The Pedigraph grogram has mechanism to deduce the gender of an individual that does not have a gender code whenever possible A fifth column must be present in the pedigree file if a trait status is to be displayed and the value indicating an affected individual must be specified in the parameter file If the pedigree file d
8. ct pedigree drawing is about only 5 as large 15 as the full pedigree drawing The pedigree size reduction is even more dramatic for a dairy population with large halfsib families unpublished data Figure 10 Comparison of compact and full pedigree drawings A Full pedigree of 2069 individuals with complex inbreeding structure B Compact pedigree drawing using summary 1 C Compact pedigree drawing using summary 2 16 4 9 Pedigree extraction Pedigraph offers pedigree extraction for a specified individual The user may select whether the siblings ancestors and or descendents of the individual for pedigree drawing A special node is used to identify the selected individual in the pedigree drawing Results of the extraction options are shown in Figure 11 Al4 O Als A21 A23 A7 A23 AT a25 a26 a27 azs az a30 A25 azs a27 azs az9 aso A B o A A13 if Ald A7 A23 ms a25 a26 a27 Cass az A30 C D E E Figure 11 Pedigree extraction for individual A23 in Figure 2 A All relatives of individual A23 are drawn using individual A23 statement in pedigraph dat B Ancestors and descendents of
9. d gender information in the input file Such individuals often are founders of the pedigree A filled node indicates an individual with a special status such as a diseased or an excellent individual or an individual with or without DNA sample All individuals in the same generation are placed in the same row and individuals in a row are ordered to reduce line crossings In some cases the generation of an individual cannot be determined and may be placed between generations Colored lines are used to connect offspring with their parents 4 1 Full pedigree drawing with default settings To illustrate the pedigree drawings using Pedigraph the pedigree file in 3 1 is used The pedigraph dat parameter file that comes with the Pedigraph software has a sign at the beginning of each line meaning that none of the options is activated The use of this parameter file without any modification will produce a full pedigree drawing using default options Figure 1 shows the full pedigree drawing using the above data and the default settings ty ete Fie mee eh e A a cle E O L A20 A19 A17 A18 A16 A22 A23 A15 A21 A24 A26 A27 Cas Cao 430 A25 Figure 1 Example of full pedigree drawing with default settings In Figure 1 individuals that with dotted orange lines do not have ancestral and gender information in the testped txt file The top four indi
10. er three color options can be used individually or jointly to draw color pedigrees Each of the last three color options can use any of the 63 colors defined in Section 3 3 Therefore the number of possible color combinations for pedigree drawing is 63 250 047 In Figure 4 A is a pedigree drawing with nocolor option and B D are 3 of the 250 047 possible color combinations for drawing color pedigrees am Sire is SOLE A B C D Figure 4 Examples of color controls A nocolor B affectedcolor yellow nodecolor red fillcolor blue C affectedcolor purple nodecolor blue fillcolor green D affectedcolor cyan nodecolor purple fillcolor pink 4 4 Unknown parents Pedigraph does not include unknown parents in the pedigree drawing by default The unknown option allows each unknown individual be drawn using a question mark A B Figure 5 Pedigree drawing for unknown parents A Unknown dam of individual 1 is not drawn default B Unknown dam of individual 1 is drawn as a question mark using unknown statement in pedigraph dat 11 4 5 Generation gap Pedigraph has an option to control the distance between nodes of two adjacent generations referred to as generation gap For certain pedigrees such as multigenerational pedigrees with relatively simple mating structures the default value for ge
11. fied the inbreeding coefficients will be printed to the screen Name of the file containing a list of pairs of individual IDs Pedigraph will compute the coancestry coefficient between each pair of individuals in the file Name of the file in which coanscestry coefficients will be printed Ifa file is not specified the coancestry coefficients will be printed to the screen Calculates coancestry coefficients between the selected individual and all relatives of the individual This must be used with individual command jointly This option print coancestry coefficients from the statements individual and coancestry to the file named output file name Draws pedigrees using arrowed lines A title to be printed on the drawing 3 3 Color definitions Codes for defining a color in the color control options in Table 1 affectedcolor fillcolor and nodecolor are given below Each of three color control statements affectedcolor fillcolor and nodecolor may use any one of the above 63 colors 4 PEDIGREE DRAWING In the pedigree drawings produced by Pedigraph each individual listed in the input file is represented by a node The shape and color of the node indicate information about the individual The label inside the node is the ID of the individual A circle indicates a female a square a male and a diamond an individual of unknown gender A dotted orange line indicates that the individual has no ancestral an
12. he calculation and display of inbreeding coefficient for each individual 0 304688 A B C D Figure 14 Display of inbreeding coefficient for regular mating systems A Inbreeding coefficients from selfing B Inbreeding coefficients from a fullsib mating system C Inbreeding coefficients from a halfsib mating system D Inbreeding coefficients from a backcross mating system 21 In Figure 14 A D are four examples of regular mating systems where the same mating scheme is applied every generation D S Falconer and T F C Mackay 1996 Introduction to Quantitative Genetics page 84 The display of inbreeding coefficients in A D shows the rate of increase in inbreeding coefficients as the number of generations increase under the four regular mating systems with the selfing system having the most rapid increase Figure 15 shows two examples of calculating and displaying inbreeding coefficient for irregular mating systems 0 046875 X 0 0605469 Figure 15 Display of inbreeding coefficients for two examples of irregular mating systems 5 2 Print inbreeding coefficients to a file The inbreeding coefficients of all individuals can be printed to a file using the statement inbreedingfile filename where filename is the name of the ou
13. he full pedigree drawing The drawing size difference between a compact pedigree and the full pedigree increases as family size increases For populations with large families the summary options can be an effective tool for the graphical visualization of the gene or disease flow in the population A E nE TA C BS B6 B7 B9 B10 B11 B14 B15 B16 B17 B19 B22 B25 B26 B27 B29 B30 B31 B32 Figure 8 Compact and full pedigree drawings A Compact drawing using summary 1 statement in pedigraph dat B Compact drawing using summary 2 statement in pedigraph dat C Full pedigree Figure 8 shows the compact pedigree drawing under each summary option and the full pedigree drawing In a compact pedigree the maximum number of nodes is four 14 for all offspring in a family Therefore as the family size increases the reduction in drawing size increases In A of Figure 8 the family with B1 and B2 as parents has 10 offspring 3 unaffected male offspring 2 affected male offspring 3 unaffected female offspring and 2 affected female offspring Offspring B12 and B3 are also parents and they are drawn in the pedigree Other offspring in the family are not parents and are not drawn in the pedigree In B
14. iduals and calculation of inbreeding and coancestry coefficients Pedigraph can display all individuals in the data set or display the number of offspring in each family by gender and trait status such as disease or normal phenotypes 2 GETTING STARTED The current version of Pedigraph can be run under two operation systems Windows and Linux 2 1 On Microsoft Windows PEDIGRAPHTo run Pedigraph on Windows open an MS DOS window and move to the directory where the Pedigraph executable is located The type the following command pedigraph pedigree file name where pedigraph stands for pedigraph exe and pedigree file name is the file name of the input pedigree file Alternatively simply double click the pedigraph exe file and type in the name of the input file at the prompt A PostScript file named output ps will be produced which contains the pedigree drawing If Adobe Acrobat Distiller is installed on the computer double click on the PostScript file will generate a PDF file of the pedigree drawing 2 2 On Linux To run Pedigraph on Linux open a Linux terminal and move to the directory where the Pedigraph executable is located Type pedigraph followed by the name of the input file to run the program A PostScript file named output ps will be produced which contains the pedigree drawing Use gv to view the Postscript file NOTE before running Pedigraph for the first time on Linux you may need to change the permissions on
15. individual A23 are drawn using individual A23 ancestors and descendents statements in pedigraph dat C Sibs of individual A23 are drawn using individual A23 and sibs statements in pedigraph dat D Ancestors of individual A23 are drawn using individual A23 and ancestors statements in pedigraph dat E Descendents of individual A23 are drawn using individual A23 and descendents statements in pedigraph dat 17 AAA ARA Sl NN A 1 AMAL A Lila r Figure 12 Pedigree of all relatives of Victoria Hanover Queen of Britain Figure 12 is extracted from the full pedigree of the European Royal Genealogical Data shown in Figure 2 using the individual ID statement The resulting pedigree when printed out in full size is about 30 feet wide and 24 feet tall which is about 11 of the main body of the full pedigree of Figure 7 The pedigree drawing of the Queen contains 3975 ancestors and 1148 descendents of the Queen The extractedoutputfile statement in pedigraph dat allows the pedigree data of the extracted individual to be printed in file For example the command extractedoutputfile extract txt will print the pedigree data of all relatives including the extracted individual to a file named extract txt The extractedoutputfile statement can be used in combination with descendants sibs a
16. le the statements coancestryfile test ids coancestryoutputfile test out will calculate coancestry coefficient for each pair of individuals in test ids file and print the coancestry coefficients in the output file named test out 23 6 3 Coancestry coefficients between a selected individual and relatives of this individual In the pedigraph dat file the coancestry statement and the individual statement will print the coancestry coefficients to an output file For example the statements individual 1000 coancestry coancestryped test out will calculate coancestry coefficient between individual 1000 and each relative and print the coancestry coefficients in the output file named test out 24
17. nd ancestors 18 4 10 Summary and extraction The summary and extraction options can be used jointly to further reduce the pedigree size by using the two options individually For example the summary option reduces the full pedigree of Figure 7 by 2 3 and the pedigree of Queen Victoria is about 11 of the full pedigree Therefore using the two options jointly the size of Queen Victoria s pedigree could be reduced to 8 of the full pedigree Figure 13 shows examples of using these two options jointly for the same data as used by Figure 11 C D Figure 13 Pedigree drawing using summary and extraction options jointly A individual A23 and summary 1 are used in pedigraph dat B individual A23 and summary 2 are used in pedigraph dat C individual A23 ancestors descendents and summary 1 are used in pedigraph dat D individual A23 ancestors descendents and summary 2 are used in pedigraph dat 19 4 11 Minimum family size The user may specify the minimum number of offspring that two parents must have for the family to be included in the pedigree drawing This is achieved by the familysize number statement in pedigraph dat where number is any integer number For example the statement
18. neration gap may be unnecessarily large The gengap statement in pedigraph dat allows custom values of generation gap Figure 6 shows two comparisons between pedigree drawings using the default and custom gengap values A B C D Figure 6 Control of generation gap in pedigree drawing A Default value of 2 2 for generation gap B The statement gengap 0 5 is used in pedigraph dat C Default value of 2 2 for generation gap D The statement gengap 0 5 is used in pedigraph dat 4 6 Tests for drawing full pedigrees of large complex populations The Pedigraph program has been tested for its capability of drawing full pedigrees of large complex populations Thus far the Pedigraph program has not failed due to population size and complexity such as complicated inbreeding structure Sample full pedigree drawings for such large complex populations are available from http animalgene umn edu The largest sample tested for full pedigree drawing was the European Royal Genealogical Data www dcs hull ac uk public genealogy royal The database is unofficial and is known to have errors but is an ideal set of data for testing Pedigraph because the population is large and complex The full pedigree contains 48 605 individuals spread out over 100 generations The sample size and complexity of this data 12 set did not cause any problems for Pedigraph The full
19. nrees 15 49 Pedigree extraction diia 17 A 10 Summary and extraction an osgan iira e o eT A A e RAEN AN NAERAA E 19 IN NA 20 4 12 Page Controls cai ad to dt dd e tdo ed ia le ae Dn de dd 21 INBREEDING COEFFICIENT ccscccssscsssccessccessccessccescccessccessccessccessecensccessecensccenscesscceesscensee 21 5 1 Dispaly of inbreeding coefficients in pedigree drawing cccesceeseeesececeeneeeseeeseeeeeeeeeseeees 21 5 2 Print inbreeding coefficients to a file ce eeceesseesseesceesceesceeceseceseceaecesecseecseecaeeeseeeeeenseeerenes 22 COANCESTRY COEFFICIENTS sviscessssseccet cessevcscosecctncscccesesteesesesstecetcscstesccoessconusccscsssenetevssounestes 23 6 1 Print coancestry coefficients On computer SCLCCN eceeecesecsseesseeeeeeseeeeceeeeeeeeseeeeeeteceseenaes 23 6 2 Print coancestry coefficients to a file 6 3 Coancestry coefficients between a selected individual and relatives of this individual 24 1 INTRODUCTION Graphical pedigree visualization is helpful for studying the relationships among individuals gene flows from generation to generation and the population structure However graphical visualization of large complex pedigrees is often a humanly impossible task Pedigraph provides rapid graphical visualization of large complex pedigrees with options for controlling colors drawing size page size and margins drawing styles extraction and highlighting of partial pedigrees involving selected indiv
20. oes not have a fifth column to define the trait status the parameter file may not activate the options affected and affectedcolor An example of the input pedigree file is shown below A23 A13 Al4 A21 A13 A9 A22 A13 A10 A20 A7 A8 A17 A7 AS Al5 A13 AS A19 A7 A8 A25 A7 A23 A26 A7 A23 A29 A7 A23 A27 A7 A23 A28 A7 A23 D E EA ge pe OFF Or ocoorcocoocoorror 3 2 Parameter file The parameter file named pedigraph dat contains Pedigraph options to allow custom pedigree drawings and analysis Each line in pedigraph dat should contain only one option Lines beginning with are ignored as are blank lines Table 1 summarizes the currently available program options The usages of these options are illustrated in PEDIGREE DRAWING Table 1 Program Options Default Value Option Name male female affected Description A string that indicates a male individual A string that indicates a female individual A string that indicates an affected individual summary individual descendants sibs ancestors extractedoutputfile affectedcolor nocolor nodecolor black Fillcolor white lightgrey familysize title unknown gengap verbose width height pagewidth pageheight nomargin Activate the summary option Specify 1 or 2 Draw the pedigree for the specified individual Draw the pedigree of the individual s offspring following individual statement Draw the pedigree
21. tput file to store the increeding coefficients The resulting output file has two columns the ID and the inbreeding coefficient of each individual On top of the file are some summary statistics The following is output file for Figure 14C 22 Inbreeding Coefficients Max 0 304688 Average 0 129688 Smallest non zero 0 125 Al 0 A2 0 A3 0 Bl 0 B2 0 B3 0 Cl 0 125 C2 0 125 C3 0 125 D1 0 21875 D2 0 21875 D3 0 21875 El 0 304688 E2 0 304688 E3 0 304688 6 COANCESTRY COEFFICIENTS Pedigraph has two options to calculate and print coancestry coefficients between two individuals Coancestry coefficient is a measure of relatedness of two individuals A list of individuals is required as the input file Coancestry coefficient for each pair of individuals is calculated and printed on computer screen or to a file 6 1 Print coancestry coefficients on computer screen In the pedigraph dat file the coancestryfile statement activates the calculation of coancestry coefficient between each pair of individuals in the file For example the statement coancestryfile test ids will calculate coancestry coefficient for each pair of individuals in test ids file and print the coancestry coefficients on the computer screen 6 2 Print coancestry coefficients to a file In the pedigraph dat file the coancestryoutputfile statement following the coancestryfile statement will print the coancestry coefficients to an output file For examp
22. viduals with diamond nodes individuals Al A2 A3 and A4 have unknown genders and their genders cannot be inferred from the data The other individuals with dotted orange lines also have unknown genders in the data but their genders are determined in the pedigree drawing based on the known genders of their mates The color lines help identify the offspring from a particular parent e g the three purple lines connecting to individual A1 show that Al has three offspring 4 2 Display of trait status The testped txt file has a fifth column defining the trait status but that column is not used in Figure 1 using the default settings The trait status can be defined as affected versus unaffected diseased versus normal or good versus bad or the availability of DNA sample of the individual To display the trait status in column 5 the affected option needs to be activated in pedigraph dat If a custom color is to be used to highlight the affected nodes the affectedcolor option also needs to be activated in the pedigraph dat file Using affected 1 and affectedcolor gold statements in pedigraph dat and the same data of Figure 1 and the full pedigree with affected individuals highlighted in gold color is produced as shown in Figure 2 As examples of color options for highlighting trait status Figure 3 shows six optional colors of affected individuals i Ag 3 A19 A17 e
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