Usage: parentage.pl -parents FILE [-options]
Given a file of individuals and parents, recursively determine the pedigree
(the parentage going back as many generations as possible) for an individual.
Can be calculated for a single indicated individual or for all in the parents file.
The parents file should be structured like this.
The individual (progeny) is on the left, and the parent(s) are on the right
indID parent1 parent2
A B C
D B C
E B F
G H - # an individual with only one parent
I - H # another individual with only one parent
Required:
-parents File listing the individuals and parents
Options:
-query ID of an individual for which to calculate parentage.
If not provided, report parentage for all individuals.
-format Output format. Options: string, table. Either or both (string,table) can be specified. [table]
-noself Remove the query ID from the parentage string.
-verbose Report some intermediate information.
-help This message.
Report the output as a table of genotype-parent-parent triples and a tree-like pedigree string
./parentage.pl -parents parents_clean1.tsv -format table,string | head -7
Hale_Ogden_#12 Ogden -
Ogden Tokyo PI_54610
Tokyo PI_8424 -
Hale_Ogden_#12: ( Hale_Ogden_#12 ( Ogden ( Tokyo ( PI_8424 , - ) , PI_54610 ) , - ) )
70653G003 Pioneer_P9594 Syngenta_S59-60
70653G003: ( 70653G003 ( Pioneer_P9594 , Syngenta_S59-60 ) )
...
Report the output as a table of genotype-parent-parent triples, with header line. This can be written to a file and used as input to the Helium pedigree viewer
./parentage.pl -parents parents_clean1.tsv -q YB57H
Genotype Female Parent Male Parent
YB57H 8377-16 W8238-02
8377-16 Pioneer_P9582 W2707-23
W2707-23 Y2011Z2 Epps
Y2011Z2 1190-02 J74-45
1190-02 Mack Forrest
W8238-02 Pioneer_P9591 Y277402
Y277402 1100-07 1190-19
1100-07 Forrest Tracy
1190-19 Mack Forrest
Here is the pedigree image generated by the Helium pedigree viewer from the input above (for -q YB57H
):
![soy_ped_YB57H](https://private-user-images.githubusercontent.com/3588740/331672729-1ebb75ed-bdda-4e5c-8bfc-6e56684bd95a.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.dBZpoo8fXXO8DvX9a6qdXHlmgmuDtDUm6fT3_xXdusk)
Here is the corresponding pedigree string, generated with ./parentage.pl -parents parents_clean1.tsv -q YB57H -format string
:
YB57H: ( YB57H ( 8377-16 ( Pioneer_P9582 , W2707-23 ( Y2011Z2 ( 1190-02 ( Mack , Forrest ) , J74-45 ) , Epps ) ) , W8238-02 ( Pioneer_P9591 , Y277402 ( 1100-07 ( Forrest , Tracy ) , 1190-19 ( Mack , Forrest ) ) ) ) )