u/dkoboldt

Hello, and thanks for posting. That error was corrected in a later release of VarScan. Please update to the newest version on GitHub

Leonor, Thank you for the question, and I apologize profusely for my delay in getting back to you. Yes, VarScan calls the most-observed variant allele in each sample. You might get better results calling samples individually. The little-known 'readcounts' command of VarScan will take a single-sample mpileup as input and generate read counts for each observed allele (including reference).

Jon, Thanks. The problem is that you're using an old version of VarScan (v2.3.9). The current version is v2.4.3. This particular bug was fixed in v2.4.0. Get the newest release on GitHub.

You're correct that mis-typed parameters are not always caught by VarScan, though user-provided parameters settings displayed when you run most commands. I'm not sure I'd call this a bug, so much as a missing feature, but I'll look into it for the next release.

I'll look into this -- would you mind posting (or sending me) the mpileup line(s) for that position?

Hello, thank you for posting. Would you mind sharing the mpileup line(s) from the malformed VCF variant?

Aidan, VarScan does not create semicolon-delimited output, with the possible exception being the INFO field when VCF output is specified. If you have true semicolon delimiters, something is very wrong! It would help enormously if you shared the first few lines of your input/output files as well as the commands being used.

Holly, You definiitely want to use bam-readcount for the fp-fiter purposes. VarScan's readcount feature operates differently and isn't designed for use with the filter (honestly I didn't think anyone used that command).