From 251b710b638da86b887685d9bfe77025ba2eb8d2 Mon Sep 17 00:00:00 2001 From: zaprily08 Date: Fri, 6 Oct 2023 09:45:50 +0100 Subject: [PATCH 1/2] update description of -seqerror --- docs/source/usage.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/source/usage.rst b/docs/source/usage.rst index 51ebfe9..06dc5f4 100644 --- a/docs/source/usage.rst +++ b/docs/source/usage.rst @@ -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. 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. + + Hybrid peeling arguments ----------------------------- :: From e018272fe6953504fda9afd70ce88f89bebd650e Mon Sep 17 00:00:00 2001 From: zaprily08 Date: Sun, 8 Oct 2023 11:17:19 +0100 Subject: [PATCH 2/2] new update description of -seqerror --- docs/source/usage.rst | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/docs/source/usage.rst b/docs/source/usage.rst index 06dc5f4..43e2b60 100644 --- a/docs/source/usage.rst +++ b/docs/source/usage.rst @@ -123,13 +123,11 @@ 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. ``-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. +The ``-error``, ``-seqerror`` and ``-length`` arguments control some of the parameters used in the model. ``-seqerror`` must 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. 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. - - Hybrid peeling arguments ----------------------------- ::