ASEReadCounter output for Indels is incorrect
Hi,
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
Regards,
Akshay
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Hi Akshay,
Thanks for your post about this tool. As mentioned in the documentation, the tool currently only supports SNPs. It's possible that in the future the GATK team might consider extending functionality to also work with INDEL data with a bit of modification, but for the moment this is not possible.
Best,
Ricky
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