miRVas FAQ
Frequently Asked miRVas questions
I get "reference mismatch" errors
This error is given when the reference allele for a variant in your input
file differs from the sequence of the reference genome at the given
position. Beware, this error message usualy indicates that you made an
error in preparing your variant file or running the analysis, and that
other variants (even those not returning the error) are also wrong.
Some of the common potential causes are:
-
The wrong reference genome was selected, e.g. variant coordinates are versus hg38 and the hg19 reference was chosen.
-
miRVaS requires genome coordinates to be in the zero based half open format., e.g.
- The first base of a chromosome is identified by begin = 0 and end = 1.
- An insertion between the first and second base in the reference is identified by begin = 1 and end = 1.
The coordinate system is extensively and nicely described in https://www.biostars.org/p/84686.
Using 1 based coordinates in miRVas causes errors.
-
Sometimes the alleles of variants are given in the reverse strand. As there is no indication of strand in the
input data, the alleles must always be given in the forward strand.
