Wrong Short Tandem Repeat size in vcf file

[pailloufat-stack]

Hi,

I work on 16 mice samples. I look at STR variants in 13 / 16 of them, which are heterozygous ; the 3 others are wild homozygous. What I'm interested in are the size differences of the STRs between these 13 samples. The STRs found in the 13 samples with the same size do not interest me.

I ran TRGT, and I created a merged VCF file. I modified it a bit to get the information I want (with the "MS" field).

I noticed some errors. For example, I have this STR (I reduce the numbers of samples to 3 to make it clearer) : I normally have three deletions in the STR with 3 different sizes :

chr2 154720638 0/6;0(0-219),0(0-75) 0/1;0(0-219),0(0-63) 0/5;0(0-219),0(0-105)

When I look at the IGV track, I have one deletion but at the same size (146pb) , which is not reflected in the VCF :

I should have : 219-75 pb = 146 pb for sample 1, 158 pb for sample 2 and 114 pb for sample 3.

Do I miss something? Best