Question: Need recommendations for Family aware Variant/indel caller for WGS data
1
gravatar for Rm
4.2 years ago by
Rm7.9k
Danville, PA
Rm7.9k wrote:

Combined calling using GATK haplotyper

SeqHBase: 

FamSeq (Peng et al. 2013): 

Triodenovo and PolyMutt (Li et al. 2012): 

MATE-CLEVER (Marschall et al. 2013): 

DeNovoGear: 

VariantMaster: 

Few more I might miss?

Please do share your experience/comparison and choice 

famseq • 1.1k views
ADD COMMENTlink modified 4.2 years ago by Len Trigg1.3k • written 4.2 years ago by Rm7.9k

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

ADD REPLYlink written 4.2 years ago by poisonAlien2.8k
2
gravatar for Len Trigg
4.2 years ago by
Len Trigg1.3k
New Zealand
Len Trigg1.3k wrote:

Absolutely give the family/pedigree calling of RTG Core a try (Cleary et.al 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 4.2 years ago by Len Trigg1.3k
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