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3. GS Amplicon Variant Analyzer Command Line Interface : 3.5 Creating and Computing a Project with the AVA-CLI : 3.5.5 Creating Variants
3.5.5
Creating Variants
If known Variants exist, they can be added to the Project using the “create variant” command (see section 3.4.4.9 for the usage statement). As was the case for Amplicons (section 3.5.4), the Reference Sequence relative to which a Variant is defined must pre-exist in the project. An example using a “here” style table is below.
create variant -file - << HERE_TERMINATOR
"Name"   "Annotation"   "Reference"   "Pattern"   "Status"
"15BP_DEL_93-107"   "Pattern entered manually"   "EGFR_Exon_19"   "d(93-107)"   "accepted"
"HAP_97C_126A"   "Created from selections"   "EGFR_Exon_18"   "s(97,C)s(126,A)"   "accepted"
"SUB_A_to_C_97"   "Created from selections"   "EGFR_Exon_18"   "s(97,C)"   "accepted"
"SUB_G_to_A_126"   "Created from selections"   "EGFR_Exon_18"   "s(126,A)"   "accepted"
HERE_TERMINATOR
Another similarity with the “create amplicon” command is that a Project can also have multiple Variants of the same name, as long as they are defined relative to different Reference Sequences. So, the “create variant” command also has both the “‑orUpdate” flag and the “‑ofRef” parameter, which functions the same way as when used with the “create amplicon” command (section 3.5.4).
The “create variant” command has an additional option used to verify the “pattern” given for the Variants being created: “‑checkPattern”. When this option is set to “true” (the default value), the “pattern” you set for each Variant is validated in three different ways.
 
1.
The pattern is first checked to make sure that it is syntactically correct.
2.
Secondly, the coordinates of the pattern are checked to make sure that they actually exist within the Reference Sequence specified for the Variant.
3.
Thirdly, any substitution code must actually create a difference at the specified position (thus, specifying s(10,C) when position 10 is already a C in the Reference Sequence would be an error).
 
If a check is conducted and any of the three validation criteria are not met, an error will be thrown. However, the check does not occur if the Variant does not have a Reference Sequence assigned to it, or if the Reference Sequence’s nucleotide sequence is empty; this allows you to add incomplete Variant definitions or to add Variant place holders before you have specified your Reference Sequences, if you so desire, without causing the “create variant” command to fail. You can also disable the “-checkPattern” option by setting it to “false”.