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Changed fisher strand bias field for VCF2Adam from SB to FS #924

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Changed fisher strand bias field for VCF2Adam from SB to FS #924

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andrewmchen
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Resolves #923. Tested on the cluster and works with VCF file generated from UnifiedGenotyper.

@AmplabJenkins
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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1066/
Test PASSed.

@heuermh
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heuermh commented Jan 20, 2016

Would both SB and FS be present in the same file?
Perhaps we should have both strandBias and fisherStrandBiasPValue as keys.

@fnothaft
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+1

@heuermh you could have both, but you should be able to recompute strand bias from the Fisher score and the allelic depth.

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fnothaft commented Feb 3, 2016

Thanks @andrewmchen! Committed as 0151b2d.

@fnothaft fnothaft closed this Feb 3, 2016
@andrewmchen andrewmchen mentioned this pull request Feb 6, 2016
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@andrewmchen @AmplabJenkins @heuermh @fnothaft