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Brian Haas

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Latest activity by Brian Haas
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    Brian Haas created a post,

    Mutect2 Tumor-only calling of variants with high AF?

    When running Mutect2 in tumor-only mode, it seems that most any variants with a high allele fraction (>0.4 or so) tend to be classified as 'germline' variants by the filtering step.  In matched tum...

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    Brian Haas created a post,

    Mutect2 PoN allele-specific or less specific position-based?

    Can you please confirm that the panel of normals is excluding variants based on chromosome position and not requiring allele-specific matching? ie. a G->A variant in the tumor sample may be filtere...

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    Brian Haas created a post,

    Current Mutect2 somatic variant PoN logic

    Can I please confirm that this is the logic being used in the current PoN creation step: ==== Any candidate PoN site must occur in at least 2 samples (as per the default for --min-sample-count). If...

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    Brian Haas commented,

    Also, can you please confirm that the panel of normals is excluding variants based on chromosome position and not requiring allele-specific matching?   ie.   a G->A variant in the tumor sample may ...

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    Brian Haas commented,

    Can I please confirm that this is the logic being used in the current PoN creation step: ==== Any candidate PoN site must occur in at least 2 samples (as per the default for --min-sample-count). If...