Gatk Vs Annovar
1
0
Entering edit mode
11.2 years ago

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

gatk annovar • 3.1k views
ADD COMMENT
0
Entering edit mode
11.2 years ago

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1920 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6