calling variants using GATK

[kjaja]

Hi All,

I was wondering about the difference between the Haplotype Caller and the Unified Genotype caller within GTAK for calling variants from exome sequencing. I know that the Haplotype Caller is slower and calls SNPs and indels att he same time but are there any advantages in using one or the other? I am looking into whether I should be using the Haplotype Caller or the Unified Genotype caller.

Thanks,

[davidblaney]

I always think broads 'best practise' advice is good

Maybe this will help: See Phase II, Section 2.

http://gatkforums.broadinstitute.org/discussion/1186/best-practice-variant-detection-with-the-gatk-v4-for-release-2-0

This may be dependent on what version of GATK you are using.

It explains how HaplotypeCaller is still experimental. I have used UnifiedGenotyper successfully but haven't tried HaplotypeCaller yet so I can't speak from experience.

Good Luck