ref_snps.vcf

ref_snps.vcf

ref_snps.vcf is an optional VCF file that contains information about small and medium local differences that do not cause alignment fragmentation. All difference locations are given in reference-based coordinates.

The following types of differences can be met in this file:

• simple insertions
• simple deletions
• simple substitution
• gap
• inserted gaps

An example of the ref_snps.vcf file:

##fileformat=VCFv4.2
##source=NucDiffv2.0
#CHROM	POS     ID      REF     ALT     QUAL	FILTER
ref_1   501     .       AAGGC   GCCTT   .       PASS
ref_1   1506    .       ACATT   NNNNN   .       PASS
ref_1   2542    .       CAAGT   C       .       PASS
ref_1   2574    .       T       TTC     .       PASS

The ref_snps.vcf file contains the following information:

VCF fields	Content	Notes
CHROM	Ref_seq name	Reference sequence name
POS	R_st	In case of insertion and deletion differences, R_st is the last reference base preceding the starting position of the difference. In case of substitutions, R_st is the starting position of the difference in the reference sequence.
ID	.	identifier field is not used
REF	ATGCN's	reference base(s)
ALT	ATGCN's	query base(s)
QUAL	.	quality field is not used
FILTER	"PASS"	filter status