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3. GS Amplicon Variant Analyzer Command Line Interface : 3.5 Creating and Computing a Project with the AVA-CLI : 3.5.7 Associating Samples with Amplicons
3.5.7
Associating Samples with Amplicons
With the Amplicon and Samples defined, we can now associate them according to the requirements of the experiment. This is done using the “associate” command (see section 3.4.1 for the usage statement). For this example, the Samples are being used to pool Amplicons from shared Reference Sequences. You can create commands to process a single Sample at a time using tabular file input (shown as a “here” block below):
assoc -sample Sample1 -file - << HERE_TERMINATOR
"amplicon"      "ofRef"
"EGFR_20_1"     "EGFR_Exon_20"
"EGFR_20_2"     "EGFR_Exon_20"
"EGFR_20_3"     "EGFR_Exon_20"
HERE_TERMINATOR
This example also illustrates how command line options are combined with tabular contents. In this case, the single given command is actually translated into the three separate commands:
assoc -sample Sample1 -amplicon EGFR_20_1 -ofRef EGFR_Exon_20
assoc -sample Sample1 -amplicon EGFR_20_2 -ofRef EGFR_Exon_20
assoc -sample Sample1 -amplicon EGFR_20_3 -ofRef EGFR_Exon_20
Alternatively, the sample name can be used as a field in the file rather than as an argument on the command line, allowing multiple Sample – Amplicon associations to be established from a single command:
assoc -file - << HERE_TERMINATOR
"sample"      "amplicon"      "ofRef"
"Sample1"     "EGFR_20_1"     "EGFR_Exon_20"
"Sample1"     "EGFR_20_2"     "EGFR_Exon_20"
"Sample1"     "EGFR_20_3"     "EGFR_Exon_20"
"Sample2"     "EGFR_18_1"     "EGFR_Exon_18"
"Sample2"     "EGFR_18_2"     "EGFR_Exon_18"
"Sample2"     "EGFR_18_3"     "EGFR_Exon_18"
"Sample3"     "EGFR_18_1"     "EGFR_Exon_18"
"Sample3"     "EGFR_18_2"     "EGFR_Exon_18"
"Sample3"     "EGFR_18_3"     "EGFR_Exon_18"
"Sample4"     "EGFR_19_2"     "EGFR_Exon_19"
"Sample4"     "EGFR_19_1"     "EGFR_Exon_19"
"Sample5"     "EGFR_20_2"     "EGFR_Exon_20"
"Sample5"     "EGFR_20_1"     "EGFR_Exon_20"
"Sample5"     "EGFR_20_3"     "EGFR_Exon_20"
"Sample6"     "EGFR_21_2"     "EGFR_Exon_21"
"Sample6"     "EGFR_21_1"     "EGFR_Exon_21"
"Sample7"     "EGFR_22_1"     "EGFR_Exon_22"
HERE_TERMINATOR
Note the “ofRef” field, used as a safety measure to make sure that the correct Amplicon is being specified, as described above (section 3.5.4). In this particular example, however, the “ofRef” field is not actually necessary since all the Amplicon names are unique within the whole Project, and is shown only for illustrative purposes.
For more uniform Projects, where the same Amplicons are measured in each Sample, an asterisk (“*”) can be used as a shortcut for the Amplicon names. This associates all the Amplicons defined in the Project at that time point with the specified Sample. You can also combine the asterisk for Amplicons with an “ofRef” to selectively associate all and only the Amplicons derived from the “ofRef” Reference Sequence with the Sample specified.
Rather than directly associating Amplicons with Samples in advance, one might consider directly associating Samples with Amplicons and particular Read Data Sets. At such time, the corresponding Sample-Amplicon associations will be implicitly made. However, this requires that the Read Data Sets be first loaded into the Project as described in the section below (3.5.8).