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numrahnumrah rochester, mnMember

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 ???


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    We had another recent report that the -dels argument was not working properly and that the tool was only emitting information for SNPs. This is in the queue to be fixed but unfortunately the developers are very busy right now, so it may be a while before they get to it. When it is fixed we will let you know.

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