I'm hoping for some inspiration on something that I suspect is not too tricky, but I would like some pointers.
I have a targeted sequencing panel for a particular phenotypic group of disorders in humans, which is run on a regular basis by our group. For each sample, we then filter a functionally annotated variant dataset (in excel, it's a small amount of variants numbering in the 100's per sample). *I'm using Annovar for the annotation part.
What I want to do is annotate either the original vcf per sample, or the Annovar annotated datasets variant list with the frequency that a given variant has been identified by our group FROM ALL PREVIOUSLY SEQUENCED SAMPLES. I would envisage that this could be achieved by either holding all variants locally in some sort of database structure and somehow using that to annotate the pre-annovar vcf, or somehow recursively loop through all vcfs for previous samples to generate allele frequency info and then use this to annotate the pre-Annovar vcf.
Any ideas would be appreciated !
Thanks
I have a targeted sequencing panel for a particular phenotypic group of disorders in humans, which is run on a regular basis by our group. For each sample, we then filter a functionally annotated variant dataset (in excel, it's a small amount of variants numbering in the 100's per sample). *I'm using Annovar for the annotation part.
What I want to do is annotate either the original vcf per sample, or the Annovar annotated datasets variant list with the frequency that a given variant has been identified by our group FROM ALL PREVIOUSLY SEQUENCED SAMPLES. I would envisage that this could be achieved by either holding all variants locally in some sort of database structure and somehow using that to annotate the pre-annovar vcf, or somehow recursively loop through all vcfs for previous samples to generate allele frequency info and then use this to annotate the pre-Annovar vcf.
Any ideas would be appreciated !
Thanks
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