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comparison vsnp_build_tables.xml @ 2:85384a9bfba2 draft

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author greg
date Thu, 30 Apr 2020 15:55:22 -0400
parents b60858c3eb91
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1:b60858c3eb91 2:85384a9bfba2
181 SNPs are sorted according to their evolutionary age within the table. The oldest SNPs (encompassing the most 181 SNPs are sorted according to their evolutionary age within the table. The oldest SNPs (encompassing the most
182 isolates) are furthest to the left. This sorting is somewhat crude - the intent is to improve readibility or 182 isolates) are furthest to the left. This sorting is somewhat crude - the intent is to improve readibility or
183 more easily match a related tree. 183 more easily match a related tree.
184 184
185 For a more detailed discussion, see the **Validating and correcting SNP calls** section of 185 For a more detailed discussion, see the **Validating and correcting SNP calls** section of
186 [the vSNP document here](https://github.com/USDA-VS/vSNP/blob/master/docs/detailed_usage.md). 186 the `vSNP documentation`_.
187
188 .. _vSNP documentation: https://github.com/USDA-VS/vSNP/blob/master/docs/detailed_usage.md
187 189
188 **Required Options** 190 **Required Options**
189 191
190 * **Choose the category for the files to be analyzed** - select "Single files" or "Collections of files", then select the appropriate history items (single SNPs json, average MQ json and newick files, or collections of each) based on the selected option. 192 * **Choose the category for the files to be analyzed** - select "Single files" or "Collections of files", then select the appropriate history items (single SNPs json, average MQ json and newick files, or collections of each) based on the selected option.
191 * **Use Genbank file** - Select "yes" to annotate the tables using the information in the Genbank file. Locally cached files, if available, provide the most widely used annotations, but more custom Genbank files can be chosen from the current history. 193 * **Use Genbank file** - Select "yes" to annotate the tables using the information in the Genbank file. Locally cached files, if available, provide the most widely used annotations, but more custom Genbank files can be chosen from the current history.