Added methods for sex determination tool #40
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Co-Authored-By: Casey Greene <cgreene@users.noreply.github.com>
Co-Authored-By: Casey Greene <cgreene@users.noreply.github.com>
Co-Authored-By: Casey Greene <cgreene@users.noreply.github.com>
Co-Authored-By: Casey Greene <cgreene@users.noreply.github.com>
Co-Authored-By: Casey Greene <cgreene@users.noreply.github.com>
Co-Authored-By: Casey Greene <cgreene@users.noreply.github.com>
Co-Authored-By: Casey Greene <cgreene@users.noreply.github.com>
Co-Authored-By: Casey Greene <cgreene@users.noreply.github.com>
Co-Authored-By: Casey Greene <cgreene@users.noreply.github.com>
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Some services use the term 'genetic sex' to refer to sex chromosome status inferred from DNA data (ref). We could use that term here.
Co-Authored-By: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Co-Authored-By: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
| We used the fraction of total normalized X and Y chromosome reads that were attributed to the Y chromosome as a summary statistic. | ||
| We reviewed this statistic in the context of reported gender and determined that a threshold of less than 0.2 clearly delineated female samples. | ||
| Fractions greater than 0.4 were predicted to be males. | ||
| Samples with values in the range [0.2, 0.4] were marked as unknown. |
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| Samples with values in the range [0.2, 0.4] were marked as unknown. | |
| Samples with values in the range [0.2, 0.4] were deemed as contaminated and removed from the dataset. |
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this reminds me - we never added manuscript text about NGScheckmate, which is our major means of QC...I will add a ticket!
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If there is another mechanism that also suggests that these samples are contaminated, that might not be the best place to discuss filtering due to contamination. An alternative explanation could be that some of these samples are from individuals with more than two sex chromosomes. I don't know that we want to go into that level of detail in this paragraph, but I don't think this is the point where we want to say that the samples are contaminated.
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Hmm good point. This sample was really removed due to NGScheckmate.
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@shrivatsk can you accept the change about contaminated samples that were removed? Thanks!
Disregard this! |
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@cgreene are you ok merging now or do you want more eyes still? |
This build is based on ac9b7cd. This commit was created by the following Travis CI build and job: https://travis-ci.com/AlexsLemonade/OpenPBTA-manuscript/builds/127903074 https://travis-ci.com/AlexsLemonade/OpenPBTA-manuscript/jobs/236217043 [ci skip] The full commit message that triggered this build is copied below: Merge pull request #40 from shrivatsk/patch-2 Added methods for sex determination tool
This build is based on ac9b7cd. This commit was created by the following Travis CI build and job: https://travis-ci.com/AlexsLemonade/OpenPBTA-manuscript/builds/127903074 https://travis-ci.com/AlexsLemonade/OpenPBTA-manuscript/jobs/236217043 [ci skip] The full commit message that triggered this build is copied below: Merge pull request #40 from shrivatsk/patch-2 Added methods for sex determination tool
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Added methods for sex determination tool
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