Determine the first and last reference base included in the STR call #68
Description
Dear @readmanchiu,
In some cases, even with short alleles, we have a discrepancy in the number of RU called versus what we see in the bam file. For instance, in one case there is a 12 RU call, where we see 8 RU in the bam file. This is the case for some of the samples, but not for all. We have the idea it may be connected to the detected RU, e.g. CTG vs GCT. We are trying to find out which sequence is seen as being the repeat. Possibly the different RUs lead to one motif continuing after an interruption and the other ending the sequence. Is there a way to see in the output data what is the total repeat called? We will now try and get an indication using Stragrl v1.5.1, however, this only works for alleles that are called and assigned to the correct allele.