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

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andrewmchen commented Jan 20, 2016

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

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AmplabJenkins Jan 20, 2016

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.

AmplabJenkins commented Jan 20, 2016

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.

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heuermh Jan 20, 2016

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

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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.

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fnothaft Jan 20, 2016

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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 Jan 20, 2016

+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 Feb 3, 2016

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Thanks @andrewmchen! Committed as 0151b2d.

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fnothaft commented Feb 3, 2016

Thanks @andrewmchen! Committed as 0151b2d.

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