I'm using Varscan to call SNPs in my mpileup files generated from RNAseq data. The signs "<" and ">" in mpileup correspond for regions that fall within pieces of a split RNA reads, and these regions are calculated in the total coverage that is in the fourth column of an mpileup file. When I look at the Varscan vcf file, I see that the total coverage per in vcf files includes those < and > (I'm not talking about low quality bases, which are nicely removed by Varscan and I can see that the coverage in vcf file is sometimes smaller than the coverage in mpileup file).
However, I think that these "split" regions should not be considered as real coverage. Does anyone know whether I can tune Varscan in such a way that it takes this into account and does not include the coverage in those "split" regions into the SNP coverage?
Thanks in advance,