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Vcf2Adam uses SB field instead of FS field for fisher exact test for strand bias #923

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andrewmchen opened this Issue Jan 20, 2016 · 1 comment

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andrewmchen commented Jan 20, 2016

https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantAnnotationConverter.scala#L86 is where the conversion attribute is defined.

Couldn't find any hard documentation on this field but I'm guessing that this SB is just the difference of the number of reads from the positive strand versus the negative strand.
I have a VCF from UnifiedGenotyper and the field that they use is for fisher exact test strand bias is
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">"

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andrewmchen Feb 6, 2016

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Closed with #924

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andrewmchen commented Feb 6, 2016

Closed with #924

@andrewmchen andrewmchen closed this Feb 6, 2016

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