Author: Alejandro A Schäffer; Eneida Hatcher; Linda Yankie; Lara Shonkwiler; J Rodney Brister; Ilene Karsch-Mizrachi; Eric P Nawrocki
Title: VADR: validation and annotation of virus sequence submissions to GenBank Document date: 2019_11_22
ID: besvz92f_23
Snippet: During each stage, specific possible problems are identified and reported in the output as "alerts". An alert is meant to inform a VADR user about an unusual, unexpected, or otherwise remarkable characteristic of a sequence. There are 43 types of alerts listed and briefly explained in Table 3 . Alerts can pertain to either the entire sequence being evaluated (indicated by "S" in the "S/F" column in Table 3 ), or a specific feature of that sequenc.....
Document: During each stage, specific possible problems are identified and reported in the output as "alerts". An alert is meant to inform a VADR user about an unusual, unexpected, or otherwise remarkable characteristic of a sequence. There are 43 types of alerts listed and briefly explained in Table 3 . Alerts can pertain to either the entire sequence being evaluated (indicated by "S" in the "S/F" column in Table 3 ), or a specific feature of that sequence (indicated by "F" in the "S/F" column). By default, 38 of the 43 alert types are fatal in that they cause a sequence to fail annotation, whereas 5 alerts are reported but not fatal. A sequence passes if and only if it generates zero fatal alerts. Nearly all alert types can be set as fatal or not fatal using the command line options --alt pass and --alt fail to v-annotate.pl, but four alert types are always fatal and cannot be changed: noannotn, revcompl, unexdivg, and noftrann.
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