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Add more options to VCF filtering. #9

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ifokkema opened this issue Aug 4, 2020 · 0 comments
Open
3 tasks

Add more options to VCF filtering. #9

ifokkema opened this issue Aug 4, 2020 · 0 comments
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@ifokkema
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enhancement New feature or request

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@ifokkema
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ifokkema commented Aug 4, 2020

VCF files can currently only be filtered for variant frequencies and some annotation (transcripts, genes).

  • It would be good to be able to filter on sequencing quality.
  • It would be good to be able to filter on GQ.
  • Determine good defaults for both.

Filtering on DP is harder because you need to take the sex chromosomes into account. How we will determine with certainty that a sample is male or female?
@ifokkema ifokkema added the enhancement New feature or request label Aug 4, 2020
@ifokkema ifokkema self-assigned this Aug 4, 2020
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