Gatk Vs Annovar

Question

[sandhya0888]

Which is better foe pooled data?GATK variant call or Syzygy variant call?

Answer 1

[Jorge Amigo]

as you don't describe exactly what you need (are you sure your samples are pooled, or is it that you want to perform multi-sample variant calling? this is not the same), I can only tell you that GATK was not designed for performing variant calling on pooled samples, but it was indeed designed and optimized for performing variant calling on large groups of samples. Syzygy states that it works with pooled samples, so if that is you case you should go for it if your only options are those 2. I can't resist mentioning the records that SeqAnswers have in their database for SNP discovery on pooled samples here.

[sandhya0888]

I wanted to know which is better to use for pooled samples.And Can you temme if Miseq variant calling uses GATK variant calling?

[Jorge Amigo]

as I said, IF variant calling on pooled samples is what you are looking for, and IF your only 2 options are GATK and Syzygy, the only one that states that works with pooled data is Syzygy, although I haven't tried it. all the experience we had trying GATK on pooled samples didn't go very good, but those were times and I really can't tell right now if playing around with its internal parameters you may be able to call pooled samples. haven't done any work on pooled samples since.

[vdauwera]

The GATK's UnifiedGenotyper is capable of calling variants on pooled data; description of specifically optmized workflow will be submitted for publication soon.