I am using ASEReadCounter to get a table of allelic counts. However, in the table generated by the tool, the indels are not properly represented.
For example, instead of outputting refAllele = AAGG altAllele = A. It outputs refAllele = A altAllele = A
Is there any way to get the correct output for Indels?
REQUIRED for all errors and issues:
a) GATK version used: 4.4
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