Need recommendations for Family aware Variant/indel caller for WGS data
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7.2 years ago
Rm 8.2k

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 • 1.4k views
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I think Scalpel can do this too. Very sensitive indel caller with high accuracy. 

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7.2 years ago
Len Trigg ★ 1.6k

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.

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