How to detect SNVs

This Single Nucleotide Variation (SNV) detection tool is built upon the MUMmer package version 3.23, to align the target genome to the reference genome and identify SNVs between the two genomes.

Input and Output

Input:

1. Reference genome in FASTA format
2. Target genome (new assembly or other genome sequence you want to compare with the reference) in FASTA format

Output: A VCF format SNV file

Output example:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
Reference      1700    nucmer  T       C       0       PASS    .
Reference      1704    nucmer  G       T       0       PASS    .
Reference      1867    nucmer  G       A       0       PASS    .
Reference      1909    nucmer  T       G       0       PASS    .
Reference      2239    nucmer  C       T       0       PASS    .
Reference      2463    nucmer  C       CC      0       PASS    .
Reference      2466    nucmer  A       G       0       PASS    .
Reference      2467    nucmer  T       C       0       PASS    .
Reference      2558    nucmer  AAG     A       0       PASS    .
Reference      2568    nucmer  G       T       0       PASS    .
Reference      2731    nucmer  T       C       0       PASS    .

Reference

For more details about MUMmer package, please go to http://mummer.sourceforge.net/