User Activity

  • Posted a comment on discussion Help on VarScan

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

  • Posted a comment on discussion Help on VarScan

    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).

  • Posted a comment on discussion Help on VarScan

    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.

  • Posted a comment on discussion Help on VarScan

    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.

  • Posted a comment on discussion Help on VarScan

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

  • Posted a comment on discussion Help on VarScan

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

  • Posted a comment on discussion Help on VarScan

    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.

  • Posted a comment on discussion Help on VarScan

    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).

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Username:
dkoboldt
Joined:
2008-07-30 15:38:57

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  • MendelScan Variant scoring and linkage mapping for family exome sequencing Last Updated:
  • Project Logo VarScan Variant detection in next-generation sequencing data Last Updated:

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