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Hello, I am using ASER Read counter on WES bam files.
I provided the flag -dels asking it to include information on indels. However I see the following problem.
My input file (-sites) has a position in the reference called "CAG" and an alternate allele called "C", which means there was a deletion.
However this is present within the output from ASEReadCounter as ref allele C and alt allele also C. If I understand it correctly the -dels option is supposed to include information on indels , but that information is not being preserved in the output, the reference still shows up only as "C". Is this expected ???