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Implement Mutect2 in the variant calling pipeline for calling somatic and germline mutations #145

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acesnik opened this issue Nov 13, 2018 · 2 comments
Open

Implement Mutect2 in the variant calling pipeline for calling somatic and germline mutations #145

acesnik opened this issue Nov 13, 2018 · 2 comments
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@acesnik
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acesnik commented Nov 13, 2018 •
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  • Mutect2 calling
  • From a combined VCF file with two genotypes {tumor, normal}, annotate the variants with SnpEff, and output a protein XML with those variations
  • Adapt Proteomics.VariantApplication in mzLib to handle generating separate protein entries for the different samples. It's built with multiple-sample VCF lines in mind...
@acesnik acesnik added this to the New projects milestone Nov 13, 2018
@zrolfs
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zrolfs commented Nov 13, 2018

I know about 50% of these words

@acesnik
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acesnik commented Nov 13, 2018

For future reference: https://github.com/smith-chem-wisc/mzLib/blob/master/Proteomics/Protein/VariantApplication.cs#L91

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