GATK VariantAnnotator -A PossibleDeNovo
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
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!
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