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update description of -seqerror #88

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Oct 8, 2023
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update description of -seqerror #88

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update description of -seqerror
zaprily08 Oct 6, 2023
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new update description of -seqerror
zaprily08 Oct 8, 2023
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4 changes: 3 additions & 1 deletion docs/source/usage.rst
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Expand Up @@ -123,11 +123,13 @@ Peeling arguments:

For hybrid peeling, where a large amount (millions of segregating sites) of sequence data needs to be imputed, first run the program in multi-locus mode to generate a segregation file, and then run the program in single-locus mode with a known segregation file.

The ``-error``, ``-seqerror`` and ``-length`` arguments control some of the parameters used in the model. |Software| is robust to deviations in genotyping error rate and sequencing error rate so it is not recommended to use these options unless large deviations from the default are known. Changing the ``-length`` argument to match the genetic map length can increase accuracy in some situations.
The ``-error``, ``-seqerror`` and ``-length`` arguments control some of the parameters used in the model. ``-seqerror`` can not be zero. |Software| is robust to deviations in genotyping error rate and sequencing error rate so it is not recommended to use these options unless large deviations from the default are known. Changing the ``-length`` argument to match the genetic map length can increase accuracy in some situations.
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@AprilYUZhang I think we best write "must not be zero";)

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Ok, I will rewrite before Monday


The ``-esterrors`` option estimated the genotyping error rate based on observed information, this option is generally not necessary and can increase runtime. ``-estmaf`` estimates the minor allele frequency after each peeling cycle. This option can be useful if there are a large number of non-genotyped founders.



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@AprilYUZhang best to avoid adding these excessive empty lines;)

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Sorry, I'm not sure when I added it. I'll pay attention next time.


Hybrid peeling arguments
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::
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