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

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?

sequencing snp variant variant-calling gatk
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updated by DG DG • written by Giovanni M Dall'Olio Giovanni M Dall'Olio

2 answers

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

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written by Charles Warden Charles Warden

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

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written by DG DG

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

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written by Giovanni M Dall'Olio Giovanni M Dall'Olio

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