"decompose_blocksub -a" position indel issue

[m-blanes]

Hello, I have the following deletion detected by Platypus, VarScan, GATK as: chr11 6411930 . CCTGGTGCTGGCG C

Then I have the same one detected by SAMtools/bcftools as: chr11 6411930 . CCTGGTGCTGGCGCTGGCGCTGGCGCTGGCGCTGGCGCTGG CCTGGCGCTGGCGCTGGCGCTGGCGCTGG

(In bold text is the deleted part in each case, which is the same)

After using "vt decompose_blocksub -a" in each case: The deletion detected by Platypus, VarScan, GATK is still the same: chr11 6411930 . CCTGGTGCTGGCG C

But the deletion detected by SAMtools/bcftools is changed to: chr11 6411931 . CTGGTGCTGGCGC C It seems that the bcftools deletion has "advanced" in one position, keeping its length.

Finally, I checked it out on IGV, and I saw that this last deletion is wrong, but it was right before the decomposition. As you can see, the first C which is not deleted corresponds to the 6411930 position, which means that the deleted part is from 6411931C to 6411942G, both included. This not what the last output shows, which has moved the deletion in one position to the right, including the last "C" which is not deleted.

I think it can possibly due to the fact that it is a high repetitive region but I am not at all sure about it. Maybe you can help me with this issue.

Thanks in advance,

Manuel.