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Use phasing information for comp. het. refinement #5

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holtgrewe opened this issue Apr 4, 2019 · 0 comments
Open

Use phasing information for comp. het. refinement #5

holtgrewe opened this issue Apr 4, 2019 · 0 comments
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enhancement New feature or request

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@holtgrewe
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holtgrewe commented Apr 4, 2019 •
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Is your feature request related to a problem? Please describe.
GATK writes out phasing information. We don't use this but it would be useful for deciphering two adjacent SNVs if they introduce a stop codon, for example.

Describe the solution you'd like
Collect all variants within a predefined windows (from command line arguments, default 50bp). Write out an output line of all combinations that lie on the same haplotype. It is sufficient to support the GATK PGT FORMAT entry for now.

Describe alternatives you've considered
N/A

Additional context
N/A
@holtgrewe holtgrewe modified the milestones: v0.23, v0.24 Jun 29, 2022
@holtgrewe holtgrewe added the enhancement New feature or request label Jun 29, 2022
@holtgrewe holtgrewe removed this from the v0.25 milestone Sep 19, 2022
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