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  • Filtering out common variants

    Hi,

    I used the GATK HaplotypeCaller to call variants on a family that is unusual; it has two affected children and one unaffected parent. The disease is expected to be caused by a homozygous or compound heterozygous mutation, and the unaffected parent is a carrier. We don't have any sequence data on the other unaffected parent. So obviously the variants I am interested in are going to be common among all three samples, i.e., child1, child2 and parent.
    I ran HaplotypeCaller on each sample seperately. I now have 3 vcf files. How can I filter the common variants among them? Could I use Annovar to do this? I have added read groups that show the relationship with tags 'c1' 'c2' and 'p' (for child1, child2 and parent).

    **Or **should I go back and rerun HaplotypeCaller but this time input all three sample files together and specify one output vcf? I am reluctant to do this as it took about 8 days for each of my HaplotypeCaller runs to finish the last time. [plus I actually have 6 families to do this on]

    Any suggestions/help appreciated!

  • #2
    You could visit www.gene-talk.de, set up a free account and upload your data.
    Afterwards you can filter for rare variants, use the inheritance filter to find comp het variants and use the annotation filter to filter out black listed artifacts...

    .. you are welcome to test all filtertools and the whole platform....

    if you find candidate variants, provide annotations that would help the community or ask an expert about its medical implications...
    Analyze Human Sequence Variants
    www.gene-talk.de

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