Question: Need recommendations for Family aware Variant/indel caller for WGS data
gravatar for Rm
3.6 years ago by
Danville, PA
Rm7.8k wrote:

Combined calling using GATK haplotyper


FamSeq (Peng et al. 2013): 

Triodenovo and PolyMutt (Li et al. 2012): 

MATE-CLEVER (Marschall et al. 2013): 



Few more I might miss?

Please do share your experience/comparison and choice 

famseq • 981 views
ADD COMMENTlink modified 3.6 years ago by Len Trigg1.2k • written 3.6 years ago by Rm7.8k

I think Scalpel can do this too. Very sensitive indel caller with high accuracy. 

ADD REPLYlink written 3.6 years ago by poisonAlien2.7k
gravatar for Len Trigg
3.6 years ago by
Len Trigg1.2k
New Zealand
Len Trigg1.2k wrote:

Absolutely give the family/pedigree calling of RTG Core a try (Cleary 2014) -- you get joint pedigree aware variant calling (more than just trios -- larger families and extended pedigrees too), automatic de novo identification all in a very fast and easy to use package.

ADD COMMENTlink written 3.6 years ago by Len Trigg1.2k
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