The perl script var_to_Reads_2_0_2.pl takes a genomic region and aggregates the data for the region from the var, coverageRefScore, evidenceInterval, evidenceDnbs and correlation files. The script then aligns the reads and qscores for each allele, and counts bases for each position. The script can be used to gather relevant information for a given variant, allowing one to drill down to the aligned reads. In addition to the perl script, the zip file provided here contains example output when the script is run with one particular region and variant as input (see the script comments for specifics). Finally, an Excel file containing the tabbed alignment for the example output is included.
Note: This script is now compatible with genomes processed with Assembly Pipeline v2.0.
Download the tool here.