How can I filter variants at the end of reads?
I have a dataset with 12 samples and many variants.
We have validated approximately 15 Mutation by Sanger and 6 of them are false positives.
All of them are located at the end of the reads, the last 5 bases.
I searched for a parameter for filtering this variants, but I oversee it or isn't there one?
I don't want to clip all reads at the end, I only want to filter out variants which are called only by the last bases of the reads.
Is this possible?
I read about the ReadPosRankSum value but samples with good reads at this position have a big influence and so I couldn't remove the false positives by this parameter.