Given this query: TCTATCGACGGACATGCTACGTA
And this reference: ATCTATCGACGGCTCATGCTACGTA
With parameters -k 16 --max-error-prob 0.01, the core library variant calling correctly identifies a substitution of GA with CTC. But the CLI writes this:
R 11 . GCTC GAG . . INDEL GT 1
There is an extra G at the start for some reason. Clearly both sides of the variant should not begin with the same letter.
Given this query: TCTATCGACGGACATGCTACGTA
And this reference: ATCTATCGACGGCTCATGCTACGTA
With parameters
-k 16 --max-error-prob 0.01, the core library variant calling correctly identifies a substitution of GA with CTC. But the CLI writes this:There is an extra G at the start for some reason. Clearly both sides of the variant should not begin with the same letter.