update description of -seqerror #88
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@AprilYUZhang thanks for this 1st PR! @XingerTang can you please review this PR - it's simple;) I will look when you give me a go ahead;) |
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docs/source/usage.rst
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| 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. | |||
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| 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
docs/source/usage.rst
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| 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.
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@AprilYUZhang see some pedantic comments above - please address those by changing code on your end, commit and push and then we can merge this PR;) |
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Thanks @AprilYUZhang. Merging this in. |
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