Hi,
I am running varscan v.2.3.9 using the following command.
java -jar ../../../VarScan.v2.3.9.jar somatic ../normal_merged.pileup ../tumor_merged.pileup output --strand-filter 1
Although, I am applying the strand-bias filter, I still get many variants with >90% strand bias. One such example is shown below. Surprisingly, this particular variant passes processSomatic and fpfilter filters.
chr1 145527972 G A 285 15 5% G 258 95 26.91% R Somatic 1.0 5.066046361888558E-15 257 195 0285 015 0
Could anyone tell me what is wrong wih my submission?
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Hi,
I am running varscan v.2.3.9 using the following command.
java -jar ../../../VarScan.v2.3.9.jar somatic ../normal_merged.pileup ../tumor_merged.pileup output --strand-filter 1
Although, I am applying the strand-bias filter, I still get many variants with >90% strand bias. One such example is shown below. Surprisingly, this particular variant passes processSomatic and fpfilter filters.
chr1 145527972 G A 285 15 5% G 258 95 26.91% R Somatic 1.0 5.066046361888558E-15 257 1 95 0 285 0 15 0
Could anyone tell me what is wrong wih my submission?
I figured it out. If there is strand bias only for the minor allele but not for the reference allele, then the strand filter applies.