GangSTR Genotyping tool

Question

[kiran]

Hello everyone,

thanks for your time.

I'm using GangSTR tool which is genome-wide profiling tandem repeats from short reads (Genotyping).

I have couple of doubts:

1. How can i know which loci reads have been re-aligned, because i'm back tracking the loci info based on reads in that position, but not sure which reads or regions have been realigned before calling the variant.

2. As we see loci info in the VCF files, in this tool i dont see any loci position where the variant has been called.

I don't know how many of them are using this tool, but hoping some one will start the discussion about this.

thanks for your time.