GATK VariantAnnotator -A PossibleDeNovo

Question

[zihanss]

Hello everybody, I am using GATK VariantAnnotator -A PossibleDeNovo to find de novo mutations in the ASD family. However, there are some errors in my command lines and I don't have the ability to handle them. Here are the command lines I use to find DNMs:

gatk VariantAnnotator -A PossibleDeNovo 
-R hg19.fa 
-V output_file_changechr.vcf 
-O output_denovo.vcf 
-ped fam.ped

And the false information is as follows:

13:07:48.098 INFO  PedReader - Phenotype is other? false

I wonder if it is my .ped file wrong? Here is my .ped file:

FAM1 AS18390 AS18414 AS18415 1 2
FAM2 AS18391 AS18417 AS18418 1 2
...

I can guarantee my .ped file's 6th "phenotype" is correct. In order to find DNMs, I should add a pedigree file to this.

So, how do I use gatk to find out de novo mutations? If you have ideas, please help me.

I will appreciate it if you help me with this problem.

Thanks in advance for the help!