Need recommendations for Family aware Variant/indel caller for WGS data

Question

[Rm]

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

[poisonAlien]

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

Answer 1

[Len Trigg]

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.