add variant calling pipeline

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add variant calling pipeline

Original issue reported on code.google.com by zack...@gmail.com on 21 Nov 2013 at 9:33

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I've added this to the pipeline, my tests show that it is not very expensive 
time-wise.

I've based it on GATK UnifiedGenotyper 2.8.1 (watch out, depends on java7!)

we now produce a vcf and a vcf.varienteval.metric.txt

the metrics are produced by reporting tool: 
http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walker
s_varianteval_VariantEval.html

Once yaping is back, I'd like for him to take check my work and advise on 
fine-tuning of params. 

currently supporting hg18, hg19 (encode), hg19 (usc), mm9. 

Original comment by zack...@gmail.com on 9 Jan 2014 at 8:26

• Changed state: Testing

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I've updated this to do indel realn 

and to use haplotypeGenotyper (HG) instead of UnifiedGenotyper (UG). 

since HG seems to be slower than UG, I've set it to only run on the 24core 
nodes, double-stacked

Original comment by zack...@gmail.com on 4 Mar 2014 at 9:11

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Original comment by zack...@gmail.com on 21 May 2014 at 7:25

• Changed state: Done