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updates to pvacseq #87

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malachig opened this issue Mar 8, 2023 · 1 comment
Open
4 tasks done

updates to pvacseq #87

malachig opened this issue Mar 8, 2023 · 1 comment
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@susannasiebert
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enhancement New feature or request

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@malachig
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malachig commented Mar 8, 2023 •
edited by susannasiebert
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We will want to make updates to support the following additions to pvacseq 3.1 and 4:

  • Support for BLAST and peptide scanning of reference proteome (peptide version is much faster) --run-reference-proteome-similarity, ....
  • Support for problematic amino acids: --problematic-amino-acids.
  • Support for --aggregate-inclusion-binding-threshold
  • Support for --allele-specific-anchors

This will require some changes to the pvacseq.wdl tool and to immuno to pass in the options.
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susannasiebert commented Mar 8, 2023 •
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  • Ensure that the phased VCF is an output
  • Incorporate coverage & readcount support for pVACfuse
  • Run Arriba in addition to AGfusion (run pVACfuse twice)
  • Switch to reference proteome fasta instead of BLASTp for reference proteome similarity

@susannasiebert susannasiebert mentioned this issue Mar 10, 2023
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@malachig malachig added the enhancement New feature or request label Mar 24, 2023
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