Include Grandparents properly into VCF

Question

[ssunderman]

Hi all,

i am currently working on a Perl-Script to detect monogenic diseses. My status right now is, that i have included the parents and the children via VCF-Files into the code and it works perfectly. My professor told me that it would be helpful too when i could include grandparents aswell.

My problem is, that i dont really now how to include them into my VCF-Files. I already read soemthing about Linkage-Format in VCF's, but i did not help me at all fixing my problem.

It would be very helpful, if someone may have an idea how to properly include grandparents into a VCF-File without hardcoding them and being clearly recognizable.

thanks in advance

[Pierre Lindenbaum]

what do you mean with 'include' an individual with a perl script ?

Answer 1

[JC]

VCF format doesn't contain any specific syntax for relationship definition, I recommend that information should be in a companion PED file, for example:

VCF:

##fileformat=VCFv4.2
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 1|0:48:8:51,51 0|0:48:8:51,51
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 0|0:49:3:58,50 0|1:49:3:58,50

PED:

##FamilyID Individually PaternalID MaternalID Sex Phenotype
F00001 NA00001 NA00004 NA00005 1 B
F00001 NA00002 NA00001 NA00003 1 B
F00001 NA00003 -9 -9 2 A
F00001 NA00004 -9 -9 1 A
F00001 NA00005 -9 -9 2 A

[Pierre Lindenbaum]

VCF format doesn't contain any specific syntax for relationship definition

well you can always use the ##SAMPLE= header https://samtools.github.io/hts-specs/VCFv4.2.pdf section 1.2.8

[JC]

##PEDIGREE=<Name_0=G0-ID,Name_1=G1-ID,...,Name_N=GN-ID>

That only adds a label, not a pedigree structure, IMHO it is limited