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Just for your records, Varscan really had a bug when filtering bases according to its quality. This happened regardless of the mpileup recalibration, since I inputted dummy pileup files created by myself. Actually, samtools also goes wrong for base quality filtering (I do not know if they fixed it, no one answered me).
Anyway, the last version of Varscan states that this was fixed. I have to thank Dan Kobold for his work and for updating his tool according to user's feedback!
Soon I will use the Varscan2, I am really interested in the somatic SNP false positive filter and in the detection of copy number changes from exome seq. I will feedback my experience!
Anyway, the last version of Varscan states that this was fixed. I have to thank Dan Kobold for his work and for updating his tool according to user's feedback!
Soon I will use the Varscan2, I am really interested in the somatic SNP false positive filter and in the detection of copy number changes from exome seq. I will feedback my experience!
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