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SNP strand bias
I'm currently trying to filter out SNPs which are not supported by forward and reverse strand. Therefore I checked the provided FS value and used a cutoff of 60 to exclude biased SNPs.
However, it seems the cutoff is a bit too high since I still got a SNP with the mutated allele beeing supported by 7 forward and 0 reverse reads. The FS value is around 40.
So my question is, is 60 really a reasonable cutoff to use ? And is there any option to get the read counts which are used to calculate the FS into the VCF output ?