miRVaS Input Format
Tab-delimited Variant File
This is a standard tab-delimited file: the first line is a header naming
the columns separated by tab characters. Next lines contain data
(variants). A tab-delimited variant file should at least contain the
genomic coordinates (in zero base, half open format), type of variant
(snp, ins or del), reference and alternative allele for the tested
variants.
miRVaS looks for the following fields (other fields may be present, but will be ignored):
- chromosome
-
A name indicating the chromosome the variant is located on. Both chr1 and 1 formats are accepted.
- begin
-
Genomic begin location of the variant.
- end
-
Genomic end location of the variant.
- type
-
Type can be snp (single nucleotide polymorphism), ins (insertion), del
(deletion).
- ref
-
The reference allele. In case of insertions, the reference allele should be empty (really empty, so no spaces).
- alt
-
The alternative or variant allele. In case of deletions, the alt allele should be empty (no spaces).
Note that insertions, even containing repeats, have to be specified in full.
Variants should be sorted using a natural sort on the genomic
coordinates (chromosome, begin, end). An example of a natural sort on
chromosomes is: chr1, chr2, chr10, chr11, chrM, chrX.
An example of a tab-delimited variant file:
chromosome begin end type ref alt
chr1 98511730 98511731 snp C T
chr1 98511733 98511733 ins CCGCTGCCGCTGCTA
chr1 98511750 98511750 ins TATATATATA
chr22 46509539 46509540 del C
You can also download the
miRNA variants used
to test the program in the paper as an example.
