This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Denovo variants

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

denovo gvcf trio
• 1,173 views • link
updated by luffy • luffy • written by shivangi.agarwal800 shivangi.agarwal800

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)

• 0 views • link
written by luffy • luffy

1 answer

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

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Log in to answer this question.

More posts like this