What Methods Do You Use For In/Del/Snp Calling? 2014 Version

Question

[Giovanni M Dall'Olio]

This question has already been asked What Methods Do You Use For In/Del/Snp Calling?, but, since during this time there have been a lot of improvements in sequencing technologies and tools, I would like to re-propose it again. Which is your favorite method to do variant calling?

I think that most people use either GATK or freebayes, and a good comparison of the two method is given in this blog article at bcbio. But what is your experience?

Answer 1

[Charles Warden]

I use VarScan2 for small indels and SNPs. I use CoNIFER for larger indels

Answer 2

[DG]

I am still mostly using GATK's UnifiedGenotyper. I am looking at moving to an ensembl calling approach though like what bcbio-variation supports.

For larger CNV analyses I am using both Conifer and FishingCNV

[Giovanni M Dall'Olio]

just for curiosity, why do you use the UnifiedGenotyper, and not for example the Haplotype caller?