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.