query_snps.vcf

query_snps.vcf

query_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 query-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 query_snps.vcf file:

##fileformat=VCFv4.2
##source=NucDiffv2.0
#CHROM    POS   ID    REF       ALT     QUAL    FILTER
query_1   501   .     GCCTT     AAGGC   .       PASS
query_1   1531  .     NNNNN     ACATT   .       PASS
query_3   501   .     C         CAAGT   .       PASS
query_3   506   .     AG        CT      .       PASS
query_3   544   .     GACTT     G       .       PASS

The query_snps.vcf file contains the following information:

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