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Consider changing from MEAN_TARGET_COVERAGE to MEDIAN_TARGET_COVERAGE for exome/panels #1719

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annaengstrom opened this issue Nov 12, 2020 · 7 comments · Fixed by #1746
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Consider changing from MEAN_TARGET_COVERAGE to MEDIAN_TARGET_COVERAGE for exome/panels #1719

annaengstrom opened this issue Nov 12, 2020 · 7 comments · Fixed by #1746
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@jemten
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Effort S Enhancement

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@annaengstrom
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Describe the bug
MIP threshold considers MEAN_TARGET_COVERAGE, however for a poor quality sample MEAN_TARGET_COVERAGE may be deviating a lot from MEDIAN_TARGET_COVERAGE.

MEDIAN_TARGET_COVERAGE is a much better measurement for covarage for poor quality samples. It also works well for good quality samples (not deviating much between MEAN_TARGET_COVERAGE and MEDIAN_TARGET_COVERAGE).

Therefore, considering changing from MEAN_TARGET_COVERAGE to MEDIAN_TARGET_COVERAGE in MIP.

The phenomenon has been observed for multiple samples/projects in BALSAMIC analysis.
@vwirta
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vwirta commented Nov 12, 2020

Good suggestion! We have noticed a big difference for low quality samples, where the MEAN is not describing the true quality of the analysis.

@jemten
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jemten commented Nov 12, 2020

Sounds good!
Is this mainly a problem with exomes or does this affect genomes as well?

@annaengstrom
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I would say TGA samples, @vwirta agreed?

@vwirta
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vwirta commented Nov 12, 2020 via email

@annaengstrom
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Tga and wes
…

I always though TGA = panel and wes ;)

@jemten jemten self-assigned this Dec 9, 2020
jemten added a commit that referenced this issue Dec 9, 2020
@jemten
feat(expected_coverage): use median coverage, fixes #1719
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@jemten jemten linked a pull request Dec 9, 2020 that will close this issue
feat(expected_coverage): use median coverage, fixes #1719 #1746
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jemten added a commit that referenced this issue Dec 9, 2020
@jemten
Merge pull request #1746 from Clinical-Genomics/feature/median_coverage
7320210 
feat(expected_coverage): use median coverage, fixes #1719
@jemten
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jemten commented Dec 9, 2020

@annaengstrom, The changes has been merged to develop and will be a part of the next release of MIP

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jemten commented Jan 19, 2021

done as of mip v9.1.2

@jemten jemten closed this as completed Jan 19, 2021
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feat(expected_coverage): use median coverage, fixes #1719 Clinical-Genomics/MIP
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@vwirta @jemten @annaengstrom