Warning "... column in variant on position was negative, adjusted to zero"

The warning

You receive the warning in the log while running VarDict like this:

Reference reverse count column in variant on position 76059796 A->ACCT was negative, adjusted to zero.

Explanation

It means, that the variant field (like Reference reverse\forward count, Variant reverse\forward count) is adjusted to zero because it was negative value. Negative values can causes errors in fisher.test of teststrandbias.R and testsomatic.R scripts, so to avoid them we adjust these counts.

Mostly this warning means alignment problems or some specific cases in Insertions and Deletions.

If you get such warning, you can create the issue in repository for better researching on the specific cause of the problem (best will be if you put for us part of BAM, BED\region and command line you used).