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FilterByOrientationBias summary table always lists that there were no variants filtered, even though there were in the VCF #3309

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LeeTL1220 opened this issue Jul 19, 2017 · 0 comments
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LeeTL1220 commented Jul 19, 2017

For example:

lichtens@OncobuntuMk6:~$ more /home/lichtens/work/ob_filtered2.tmp.vcf.summary 
Sample	Artifact_Mode	Artifact_Mode_Complement	OBQ	Num_Artifact_Mode	Num_Artifact_Mode_Filtered	Num_Not_Artifact_Mode	Num_NonRef_Passing_Variants
SAMPLE1Tumor	C>T	G>A	42.68076887123618	82339	0	205577	287916
SAMPLE1Tumor	G>T	C>A	32.01295410609514	36517	0	251399	287916
lichtens@OncobuntuMk6:~$ egrep orientation_bias /home/lichtens/work/ob_filtered2.tmp.vcf | wc -l
26279

Not high priority.

Just stems from the VariantContext now being filtered as well as the genotype. Fix can be placed in OrientationBiasUtils.getGenotypeStream

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