Updating general calling pipeline to work with newer HC and UG arguments and filtering

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-- Use default VQSR params of QD, FS, DP and MQ for SNPs, with ReadPosRankSum and HaplotypeScore for UG SNPs
-- Add combine variants to GeneralCallingPipelin
-- Fix incorrect intervals in HaplotypeCaller in GeneralCallingPipeline.scala
-- GCP now emits tables for VCFs by default
-- GCP runs HC first before UG
-- GeneralCallingPipeline now jointly calls input BAMs, not separately processes them.  Ready to handle CEU trio calling
-- Assess NA12878 on the particularly well reviewed 10-11mb in addition to all of 20
-- Use 4G for HC

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This commit is contained in:

Mark DePristo 2013-03-03 18:29:47 -05:00

parent 1fae750ebe

commit 559a4bc05d

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