Denovo variants

Question

[shivangi.agarwal800]

Hi Guys,

Can anyone let me know the protocol/steps to identify Denovo variants from input files as father.gvcf, mother.gvcf & proband.gvcf (trio) ? I am aware about possibledenovo function in GATK but that requires a pedigree (.ped) file. So, I wondering how to generate a .ped file from gvcf I have. Any help is appreciated.

Thanks in Advance

[luffy]

As @pierre already said ped file or pedigree file is a text file which must contain 6 mandatory columns such as Family ID, Individual ID, Paternal ID, Maternal ID, Sex (1=male; 2=female), Phenotype (1 unaffected, 2 affected)

Answer 1

[Pierre Lindenbaum]

You don t generate any pedigree with gatk. The pedigree is just a text file describing the families. You can just create it with any text editor