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The chrx_het_hom column has no values #64

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Nicolai-vKuegelgen opened this issue Jan 25, 2024 · 1 comment
Open

The chrx_het_hom column has no values #64

Nicolai-vKuegelgen opened this issue Jan 25, 2024 · 1 comment
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bug Something isn't working

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@Nicolai-vKuegelgen
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Describe the bug

When using ngs-chew serve on a collection of npz-files the chrx_het_hom column of the calculated dataframe has no values (all entries are None) and the corresponding column/variable in the dash app ("het/hom calls on chrX") can also not be used.

To Reproduce
Using ngs-chew 0.9.2. (+ dash / dash-bootstrap-components 1.5)
Steps to reproduce the behavior:

  1. run ngs-chew serve --strip-suffix suffix ped_example.ped *.npz
  2. The "chrx_het_hom" column in the logged data frame will only show 'None'
  3. The "het/hom calls on chrX" column/variable in the dash app is empty

Expected behavior
The values should be calculated and available.

@Nicolai-vKuegelgen Nicolai-vKuegelgen added the bug Something isn't working label Jan 25, 2024
@holtgrewe
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Our chrX calls are too few (864). Probably that can't be helped and the chrX fraction of reads is more informative. We should probably just remove writing out that feature.

holtgrewe added a commit that referenced this issue Feb 19, 2024
The RS identifiers are not annotated and not stable. However,
the stable ones for chrX turned out to have too few positives
for the molecular sex determination.
holtgrewe added a commit that referenced this issue Feb 19, 2024
The RS identifiers are not annotated and not stable. However,
the stable ones for chrX turned out to have too few positives
for the molecular sex determination.
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